New Calendar Celebrates 50 Years of the PDB
12/31/2020
The PDB was announced on October 20, 1971 in Crystallography: Protein Data Bank Nature New Biology 233: 223 (1971) doi: 10.1038/newbio233223b0.
Fifty years later, the PDB archive contains >170,000 structures of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. It is managed by the Worldwide PDB (wwPDB) organization that ensures that the PDB is freely and publicly available to the global community.
RCSB PDB and wwPDB will celebrate this golden anniversary with symposia and events throughout 2021.
Registration for the May 4-5 virtual symposium will be open later this month. This event will include presentations from speakers from around the world who have made tremendous advances in structural biology and bioinformatics. Students and postdoctoral fellows are especially encouraged to attend and will be eligible for poster awards.
During this fiftieth anniversary year, consider supporting the PDB's spirit of openness, cooperation and education with a donation to the wwPDB Foundation.
The wwPDB Foundation was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB40, a symposium celebrating the 40th anniversary of the archive; workshops; and educational publications.
Season's Greetings
12/28/2020
The PDB was announced on October 20, 1971 in Crystallography: Protein Data Bank Nature New Biology 233: 223 (1971) doi: 10.1038/newbio233223b0.
Today, the PDB archive contains ~170,000 structures of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. It is managed by the Worldwide PDB (wwPDB) organization that ensures that the PDB is freely and publicly available to the global community.
wwPDB will celebrate the golden anniversary with symposia and events in 2021. The websites wwpdb.org/pdb50 and RCSB.org/pdb50 will be updated with announcements and resources throughout the year.
As the fiftieth anniversary approaches, consider supporting the PDB's spirit of openness, cooperation and education with a donation to the wwPDB Foundation.
The wwPDB Foundation was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB40, a symposium celebrating the 40th anniversary of the archive; workshops; and educational publications.
The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, charitable, and educational purposes.

Celebrating 20 Years of Molecule of the Month
12/22/2020
Since 2000, the RCSB PDB Molecule of the Month series has introduced millions of visitors to the shape and function of the 3D structures archived in the Protein Data Bank.
Created and illustrated by David S. Goodsell (RCSB PDB-Rutgers and The Scripps Research Institute), this feature tells stories about molecular structure and function, their diverse roles within living cells, and the growing connections between biology and nanotechnology. The growth and popularity of the column led to the development of the PDB-101 educational website. Molecule of the Month content has inspired readers around the world, and is a regular read for students and researchers alike. Columns are so compelling that they have been accessed nearly a million times in 2019.
To celebrate this milestone 20th anniversary, Goodsell’s column for January 2020 offered a personal meditation on the growing revolution in structural biology that provides these amazing glimpses into biology.
Then an article published in BAMBed reflected on the history, usage, and community surrounding this key RCSB PDB series.
David S. Goodsell, Christine Zardecki, Helen M. Berman, Stephen K. Burley
Insights from 20 years of the Molecule of the Month
(2020) BAMBed 48: 350-355 doi: 10.1002/bmb.21360
The celebration continued all year long--the 2020 calendar highlighted the top-accessed articles year after year, culminating in the highest-ranked articles Hemoglobin and Catalase.
Scientific Software Developers and Postdocs
12/15/2020

SARS-CoV-2 mRNA Vaccine
12/09/2020
New in the series Resources to Fight the COVID-19 Pandemic: SARS-CoV-2 mRNA Vaccine.

Image: SARS-CoV-2 mRNA Vaccine, 2020
David S. Goodsell, RCSB PDB
doi: 10.2210/rcsb_pdb/goodsell-gallery-027
Structural Biology and Nobel Prizes
12/07/2020
Since its inception, many awards have recognized achievements made in molecular biology, structural biology, and related research.
Browse PDB-101 to explore the structures and methods behind these Prizes.
A list of Nobel prizes and related Molecule of the Month articles is available.
Molecular Origami: Green and Red Fluorescent Proteins
12/01/2020
To build these paper models, download and print the template PDFs. An instructional video and related activity are available.
Biocurator Explores SARS-CoV-2 Proteins in Virtual Reality
11/24/2020
Using Nanome software, people can meet in virtual reality and explore molecular data loaded from the PDB.
Recently, biocurator Gregg Crichlow met with Steve McCloskey went inside Nanome to explore two key complexes that could help researchers identify and develop effective therapeutics: the spike protein bound to its receptor, angiotensin-converting enzyme 2 (ACE2), and the spike protein bound to antibodies. Read more about the visit, or watch them on YouTube.
Video: Neuronal Signaling and Sodium-Potassium Pump
11/17/2020

Molecular Landscapes: Coronavirus
11/05/2020
This painting depicts the fusion of SARS-CoV-2 (magenta) with an endosomal membrane (green), releasing the viral RNA genome into the cell cytoplasm (blue), where it is beginning to be translated by cellular ribosomes to create viral polyproteins. The painting includes speculative elements that are designed highlight the process, most notably, multiple states of the viral spike protein are shown.
Goodsell's molecular landscapes are available from PDB-101 in a special SciArt Digital Archive. These watercolor paintings integrate information from structural biology, microscopy and biophysics to simulate detailed views of the molecular structure of living cells. These illustrations are free for use under CC-BY-4.0 license. Acknowledgement should be given as indicated for each illustration.
This painting was created as part of the show New Ways of Living: Understanding the Science of COVID-19 in association with SciCommMake 2020.
American Public Health Association Film Festival
10/25/2020
The APHA Annual Meeting and Expo is the largest and most influential yearly gathering of public health professionals, bringing the public health community together to experience robust scientific programming, networking, social events, poster sessions and more.
This year's virtual meeting will take place October 24-28, 2020.
The video Fighting Coronavirus with Soap by Maria Voigt has been selected to be screened along with other films and PSAs in the COVID-19 session on October 27.

The video has been viewed more than 425,000 times since its release on March 18, 2020.

PDB Turns 49
10/20/2020
The PDB was announced on October 20, 1971 in Crystallography: Protein Data Bank Nature New Biology 233: 223 (1971) doi: 10.1038/newbio233223b0.
Today, the PDB archive contains ~170,000 structures of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. It is managed by the Worldwide PDB (wwPDB) organization that ensures that the PDB is freely and publicly available to the global community.
wwPDB is celebrating by looking ahead to golden anniversary symposia and events planned for 2021. The website wwpdb.org/pdb50 will be updated regularly.
As the fiftieth anniversary approaches, consider supporting the PDB's spirit of openness, cooperation and education with a donation to the wwPDB Foundation.
The wwPDB Foundation was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB40, a symposium celebrating the 40th anniversary of the archive; workshops; and educational publications.
The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, charitable, and educational purposes.
Happy Birthday, Irving Geis
10/18/2020


Irving Geis (October 18, 1908-July 22, 1997) was a gifted artist who helped illuminate the field of structural biology with his iconic images of DNA, hemoglobin, and other important macromolecules. To celebrate Irving Geis' birthday, we invite you to tour the Geis Digital Archive.
Through a collaboration with the Howard Hughes Medical Institute (HHMI), which owns the Geis Archives, RCSB PDB has established a digital archive of Geis' molecular art. This resource displays many of Geis' illustrations in the context of the corresponding PDB structures and related molecular information. These images are also made available for download for noncommercial usage.
Under the direction of RCSB PDB team members, the Geis Digital Archive is being developed by undergraduates. Students created modern visualizations of the molecules featured in Geis' work, and researched the structures to provide background and supporting information about the illustrations. Alex Alvarado (University of Southern California) and Nicole Werpachowski (Fordham College at Lincoln Center) created the initial design of the resource as part of their Rutgers RiSE (Research in Science and Engineering) experience. Their work was funded during the summer of 2015 by an NSF REU. Rutgers students Belle Lin (2015-2016) and Christopher Markosian (2015-2016) continued work on the project. In 2016, Raheel Ahmad (Rutgers), Pamela Amechi (University of Maryland Baltimore Country), and Keyerra Daniels (Winthrop University) expanded the archive as part of the Rutgers RiSE program.
Thanks to the Howard Hughes Medical Institute for their work on this project. Questions about the HHMI Geis Archives should be sent to archives@hhmi.org.





Join Us at the STEMteachersEXPO
10/16/2020
RCSB PDB will be teaming up with Biochemistry Literacy for Kids and Schrödinger to present a session on Strengthening Virtual Chemistry and Biology Instruction Through 3D Modeling as part of the GENERAL STEM Block D on Saturday, October 24 at 5:45-7:15 PM EDT.
Fall Newsletter Published
10/13/2020
The Fall 2020 issue of the RCSB PDB Newsletter is now online.
This issue highlights new publications; updated validation reports; exploring sequence-structure relationships; from Boot Camp to Poster Prize; and more.
The Education Corner by medical illustrator Veronica Falconieri Hays, MA, CMI (Falconieri Visuals) describes Using PDB Structures to Visualize Science.
Sign up to receive electronic updates each quarter.
Dexamethasone and Cytokine Storms
10/12/2020

A new article, Dexamethasone and Cytokine Storms, describes how to prevent too much of a good thing during SARS-CoV-2 infection.
Written by Molecule of the Month creator David Goodsell, this article is part of a PDB-101 series called Resources to Fight the COVID-19 Pandemic that provides an introduction to how the biological macromolecules in the PDB are driving research and discovery related to SARS-CoV-2.
2020 Nobel Prize in Chemistry
10/07/2020
PDB structures help illustrate this process. Visit PDB-101 to learn more about Cascade and CRISPR at Molecule of the Month.
Browse PDB-101 to explore articles and resources that highlight many of the PDB structures and related experimental techniques associated with Nobel Prizes, including a timeline of awards made in Chemistry, Physiology or Medicine, and Physics and corresponding Molecule of the Month articles.
PDB-101 features on the 2020 Nobel Prize in Physiology or Medicine that was awarded jointly to Harvey J. Alter, Michael Houghton and Charles M. Rice for the discovery of Hepatitis C virus will be added in the future.
Award-Winning Image
10/06/2020

This image of RNA Polymerase by RCSB PDB's Maria Voigt was selected as a national finalist in the 2019 Wiki Science Competition in the United States. The jury selected 36 finalists across six categories from 1,144 submissions.
RNA polymerase (purple) is a complex enzyme at the heart of transcription. During this process, the enzyme unwinds the DNA double helix and uses one strand (darker orange) as a template to create the single-stranded messenger RNA (green), later used by ribosomes for protein synthesis. From the RNA polymerase II elongation complex of Saccharomyces cerevisiae (PDB Structure 1i6h) as seen in PDB-101's What is a Protein? series.
This image, one of PDB-101's award-winning creations, is available for download as part of the Poster Collection.
Structural Biology and Nobel Prizes
09/29/2020
The Nobel Prize highlights achievements in physics, chemistry, physiology or medicine, literature and for peace. This year's prizes will be announced starting October 5, 2020.
Since its inception, many awards have recognized achievements made in molecular biology, structural biology, and related research.
Browse PDB-101 to explore articles and resources that highlight many of the PDB structures and related experimental techniques associated with Nobel Prizes, including a timeline of awards made in Chemistry, Physiology or Medicine, and Physics and corresponding Molecule of the Month articles.

Poster Prize Awarded at ACA
09/24/2020
At this year's American Crystallographic Association's Annual Meeting, the RCSB PDB Poster Prize award went to Takahiro Yamauchi for Crystal and Solution structures of Proliferating Cell Nuclear Antigen from Crenarchaeon aeropyrum pernix.
Crystal and Solution structures of Proliferating Cell Nuclear Antigen from Crenarchaeon Aeropyrum pernix
Takahiro Yamauchi (Iryo Sosei University and Fukushima Rosai Hospital, Japan), Tsubasa Takemori, Makiko Kikuchi, Yasuhito Iizuka, Satoshi Ishikawa, and Masaru Tsunoda (Iryo Sosei University)
The judges also awarded an Honorable Mention to Ravi Yadav (Purdue University) for
Structural basis of Neisserial lactoferrin binding protein B function
Ravi Yadav (Purdue University), Srinivas Chakravarthy (Argonne National Laboratory), Courtney Daczkowski (Purdue University), Nicholas Noinaj (Purdue University)

Many thanks to Poster Prize Chairs Louise Dawe (Wilfrid Laurier University) and Tiffany Kinnibrugh (Argonne National Laboratory) and the judges.
Poster Prize Awarded at ISMB
09/20/2020
At this year's meeting of the Intelligent Systems for Molecular Biology Conference (ISMB)/European Conference on Computational Biology, the award went to Aya Narunsky for How proteins evolved to recognize an ancient nucleotide.
How proteins evolved to recognize an ancient nucleotide? Aya Narunsky (Yale University), Amit Kessel (Tel-Aviv University), Ron Solan (Tel Aviv University), Vikram Alva (Max Planck Institute for Developmental Biology), Rachel Kolodny (University of Haifa), and Nir Ben Tal (Tel-Aviv University)
Proteins’ interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein–adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction. Our analysis extends the known motifs of protein–adenine interactions in the Watson–Crick edge of adenine and shows that all of adenine’s edges may contribute to molecular recognition. We further show that, on the proteins' side, binding is often mediated by specific amino acid segments (“themes”) that recur across different proteins, such that different proteins use the same themes when binding the same adenine-containing ligands. We identify numerous proteins that feature these themes and are thus likely to bind adenine-containing ligands. Our analysis suggests that adenine binding has emerged multiple times in evolution.
Abstract taken from: Narunsky, A., Kessel, A., Solan, R., Alva, V., Kolodny, R., & Ben-Tal, N. (2020). On the evolution of protein-adenine binding. Proc Natl Acad Sci USA 117: 4701–4709. doi: 10.1073/pnas.1911349117
Many thanks to Steven Leard (ISMB) for his continued support. This year's prize was judged by RCSB PDB's Stephen K. Burley and Sebastian Bittrich.

Respiratory Droplet
09/15/2020

A new painting by David S. Goodsell shows a cross section through a small respiratory droplet, like the ones that are thought to transmit SARS-CoV-2.
Goodsell's molecular landscapes are available from PDB-101 in a special SciArt Digital Archive. These watercolor paintings integrate information from structural biology, microscopy and biophysics to simulate detailed views of the molecular structure of living cells. These illustrations are free for use under CC-BY-4.0 license. Acknowledgement should be given as indicated for each illustration.
Virtual Boot Camp
09/08/2020
An intensive online learning experience hosted by RCSB PDB and the Rutgers University Institute for Quantitative Biomedicine introduced students to Structural Bioinformatics by focusing on the main protease structure of SARS-CoV-2. At the end, the student researchers understood how the protein evolved during the first six months of the COVID-19 pandemic by exploring amino acid sequence and 3D atomic-level structure.
The materials used in this boot camp are available online at covid19-bootcamp.rcsb.org and have been described in
Virtual Boot Camp: COVID‐19 evolution and structural biology
Stephen K. Burley, Yana Bromberg,Paul Craig, Siobain Duffy, Shuchismita Dutta, Bonnie L. Hall, Brian P. Hudson, Jennifer Jiang, Sagar D. Khare, Julia R. Koeppe, Joseph H. Lubin, Stephen A. Mills, Michael J. Pikaart, Rebecca Roberts, Vidur Sarma, Jitendra Singh, Jay A. Tischfield, Lingjun Xie, Christine Zardecki
Biochem Mol Biol Educ. 2020;1–3. doi: 10.1002/bmb.21428
Many thanks to
- Many thanks to
- The Boot Camp students for their willingness to join us on this adventure
- IQB Faculty and Graduate Students: Stephen K. Burley, Shuchismita Dutta, Brian Hudson, Jennifer Jiang,
- Sagar Khare, Joseph Lubin, Vidur Sarma, Lingjun Xie, Christine Zardecki
- IQB's Ken Dalenberg for technical oversight
- BASIL: Biochemistry Authentic Scientific Inquiry Laboratory) biochemistry consortium faculty: Paul Craig (Rochester Institute of Technology), Bonnie Hall (Grand View University), Julia Koeppe (SUNY Oswego), Stephen Mills (Xavier University), Mike Pikaart (Hope College), Rebecca Roberts (Ursinus College)
- RISE at Rutgers: a nationally acclaimed summer research program for outstanding undergraduates from diverse backgrounds
- Rutgers Faculty Lectures: Yana Bromberg (SEBS), Siobain Duffy (SEBS), Jay Tischfield (SAS/RUCDR)
This Boot Camp was supported by
- RCSB Protein Data Bank
- Institute for Quantitative Biomedicine
- National Science Foundation
- National Institute of General Medical Sciences
- US Department of Energy
- Rutgers NIH Biotechnology Training Program, NIH T32 GM008339 (for JL)
Congratulations, Sophia!
09/01/2020

Sophia Staggers (Frostburg State University) presented her poster Understanding the evolution of SARS-CoV-2 non-structural protein 15 (Nsp15) in 3D at the 2020 American Crystallographic Association virtual meeting and was recognized with the 2020 MiTeGen-Society of Physics Students Undergraduate Poster Prize.
Sophia Staggers originally planned to spend her summer with the RCSB PDB team at Rutgers University as part of the Research Intensive Summer Experience (RISE) at Rutgers program.
When RISE moved to a virtual experience, Sophia participated in a one-week Boot Camp hosted by RCSB PDB and the Rutgers Institute for Quantitative Biomedicine explored how the SARS-CoV-2 main protease evolved during the first six months of the COVID-19 pandemic by exploring amino acid sequence and 3D atomic-level structure.
Over the following five weeks, Sophia and other students used their training to study the other proteins in the coronavirus.
Sophia was supported by an NSF REU to the RCSB PDB.
Download Molecular Landscapes
08/24/2020

This painting by David S. Goodsell shows a cross section through SARS-CoV-2 surrounded by blood plasma, with neutralizing antibodies in bright yellow. It was commissioned for the cover of a special COVID-19 issue of Nature.
Goodsell's molecular landscapes are available from PDB-101 in a special SciArt Digital Archive. These watercolor paintings integrate information from structural biology, microscopy and biophysics to simulate detailed views of the molecular structure of living cells. These illustrations are free for use under CC-BY-4.0 license. Acknowledgement should be given as indicated for each illustration.
Resources to Fight the COVID-19 Pandemic
08/18/2020

A new feature article, The Search for Drugs to Fight COVID-19, describes how purified antibodies may be used to treat infection by coronavirus.
Written by Molecule of the Month creator David Goodsell, this article is part of a new PDB-101 series called Resources to Fight the COVID-19 Pandemic that will provide an introduction to how the biological macromolecules in the PDB are driving research and discovery related to SARS-CoV-2.
Integrative Illustration for Coronavirus Outreach
08/11/2020

Integrative illustration for coronavirus outreach (2020) PLoS Biol 18: e3000815 doi: 10.1371/journal.pbio.3000815
Since the release of the first PDB structure from SARS-CoV-2 (PDB structure 6lu7), educational materials including molecular landscape paintings, downloadable illustrations, and a video demonstrating the effects of hand washing at the molecular level have been released into a Coronavirus Collection at PDB-101.
A new publication describes scientific sources used in the creation of the painting Coronavirus Life Cycle, and provides examples of the digital dissemination of this painting and related materials and a discussion of the public response.
Goodsell DS, Voigt M, Zardecki C, Burley SK (2020) Integrative illustration for coronavirus outreach. PLoS Biol 18(8): e3000815. doi: 10.1371/journal.pbio.3000815
Explore the collection of coronavirus-related educational materials at PDB-101.
Insights from 20 Years of the Molecule of the Month
08/04/2020
Since 2000, the RCSB PDB Molecule of the Month series has introduced millions of visitors to the shape and function of the 3D structures archived in the Protein Data Bank.
Created and illustrated by David S. Goodsell (RCSB PDB-Rutgers and The Scripps Research Institute), this feature tells stories about molecular structure and function, their diverse roles within living cells, and the growing connections between biology and nanotechnology. The growth and popularity of the column led to the development of the PDB-101 educational website. Molecule of the Month content has inspired readers around the world, and is a regular read for students and researchers alike. Columns are so compelling that they have been accessed nearly a million times in 2019.
A new article in BAMBed reflects on the history, usage, and community surrounding this key RCSB PDB series.
David S. Goodsell, Christine Zardecki, Helen M. Berman, Stephen K. Burley
Insights from 20 years of the Molecule of the Month
(2020) BAMBed 48: 350-355 doi: 10.1002/bmb.21360
RCSB PDB has been celebrating this anniversary all year long--the 2020 calendar highlights the top-accessed articles year after year, culminating in the highest-ranked articles Hemoglobin and Catalase.
Goodsell’s column for January 2020 offers a personal meditation on the growing revolution in structural biology that provides these amazing glimpses into biology.

Summer Newsletter Published
07/28/2020
The Summer 2020 issue of the RCSB PDB Newsletter is now online.
This issue highlights RCSB PDB in the Time of COVID-19; improving carbohydrates; retiring Legacy Web Services; and more.
The Education Corner by Suzanne Duce (University of Dundee, Scotland) describes A Secondary School Bioinformatics Workbook for Visualizing DNA, RNA and Proteins.
Resources to Fight the COVID-19 Pandemic
07/21/2020

A new feature article, Passive Immunization with Convalescent Antibodies, describes how purified antibodies may be used to treat infection by coronavirus.
Written by Molecule of the Month creator David Goodsell, this article is intended to be part of a series of features that will provide an introduction to how the biological macromolecules in the PDB are driving research and discovery related to SARS-CoV-2.
Impact of the Protein Data Bank Across Scientific Disciplines
06/30/2020

This study is the result of a research performed by Natalie Verdiguel (University of Central Florida) during her Research Intensive Summer Experience (RISE) at Rutgers. Working with RCSB PDB developer Zukang Feng, Natalie designed this analysis of the set of data citation information.
They found that nucleosome structure 1aoi was the most-cited structure in the archive overall, followed by potassium channel (1bl8), bacteriorhodopsin (1brd), rhodopsin (1f88), major histocompatibility class I (1hla), MDM2/imidazoline inhibitor (1rv1), thrombin (2v3o/2v3h), serum albumin (1uor), and ATP Synthase F1 (1bmf).
For more, see Impact of the Protein Data Bank Across Scientific Disciplines Zukang Feng, Natalie Verdiguel, Luigi Di Costanzo, David S. Goodsell, John D. Westbrook, Stephen Burley, and Christine Zardecki (2020) Data Science Journal 19: 25 doi: 10.5334/dsj-2020-025.
The 2020 RISE at Rutgers scholars are working remotely with Rutgers faculty this summer. Students working with the RCSB PDB are focusing on SARS-CoV-2 structures in the PDB.
PDB-101 Coronavirus Resources
06/23/2020
Coronaviruses are a persistent threat to health of the global community. Viruses such as SARS, MERS, and the new SARS-CoV-2 emerge from animal populations and infect humans. Coronaviruses contain an exceptionally large genome that encodes several dozen viral proteins. Structures of these proteins are used to develop new drugs and new approaches to creating vaccines to fight coronaviruses.
A new section of the PDB-101 website collects all materials related to coronaviruses, including molecular landscape paintings, a Molecule of the Month feature on coronavirus proteases, and a video on Fighting Coronavirus with Soap. Materials will be added to this Coronavirus Browser as they are developed. These resources are free for use.
Download coronavirus-related Molecular Landscapes by David S. Goodsell
RCSB PDB in the Time of COVID-19
06/16/2020
Biocuration
The first SARS-CoV-2 structure, main protease (PDB ID 6lu7), was deposited on January 26, 2020 and was immediately biocurated so that it could be included in the earliest possible weekly update of the PDB.
Since then, more than 200 COVID-19-related structures have been submitted to the PDB archive. Each entry has been quickly biocurated by wwPDB biocurators following these “guiding principles”:
- Biocuration of COVID-19 structures is prioritized over that of other structures, including post-release revisions such as citation updates
- Authors are encouraged to release their structures immediately
- Consistent taxonomy name and ID (Severe acute respiratory syndrome coronavirus 2; 2697049) are applied to all COVID-19 structures
- Consistent UniProt referencing is incorporated: P0DTD1, P0DTC1, P0DTC2, P0DTC9
All released SARS-CoV-2 structures and related resources are highlighted at http://RCSB.org/covid19.
Data Access and Exploration
A major focus of the development team during the past year has been improvement of the RCSB.org website architecture to significantly revise and improve tools for searching and exploring PDB data. Working remotely, the team has been able to release the next generation of RCSB PDB tools, including search functionality that combines text, sequence, and coordinate queries. Other new and improved features include
- Basic Search available from the search box at the top of every RCSB PDB website page
- Advanced Search Boolean options
- Display of Advanced Search results for PDB structures, assemblies, or unique polymeric molecular entities (unique sequences)
- Left sidebar menus for refining Search Results
- Stored Search History
- New MyPDB features, including registration using Google, Facebook, or ORCID authentication, and email notifications of stored searches
- Improved Download Tool for downloading data files in batches
- New GraphQL and REST APIs for accessing and searching PDB data
- Sequence motif search
These tools can be used to search and analyze SARS-CoV-2 structures in the context of other structures in the PDB, including those from SARS and MERS.
Additional features will be made available soon, including Custom Tabular Reports, Chemical Component Search tool, access to SDF files, and more.
Outreach and Education
To coincide with the release of the first SARS-CoV-2 structure (6lu7), the February Molecule of the Month focused on the Coronavirus Main Protease.
Since then, materials including molecular landscape paintings, downloadable illustrations, and a video demonstrating the effects of hand washing at the molecular level have been released into a Coronavirus Collection at PDB-101.
New features are being developed, such as the June Molecule of the Month article on the Coronavirus Spike Protein.

Coronavirus CellPAINT Contest Winners
06/08/2020
CellPAINT can be used to create drawing pictures of cellular and viral systems. The Scripps Research Center for Computational Structural Biology (CCSB) in association with RCSB PDB hosted an coronavirus image contest created using CellPAINT in the categories of Science and Art. Dozens of entries were submitted from around the world from middle school students to professionals.
Best in Science

I started using CellPAINT (web-based) to design the illustration. When I finished with the diagram, I used Adobe Photoshop CC 2019 to create the labels and correct the colors. As the receptor TMPRSS2, present in the target cell and very important in the viral priming, is not present in CellPAINT, I decided to look for a serin protease like protein in the PDB and to add it with this program.
Best in Art

The contest came forth at a time when almost everyone is struggling with the changes accompanying the pandemic. Each of us are grappling with one or another grief and ‘hoping’ for something good to happen. This contest was a way for me to get out of my own grief and create something that would be a source of joy not only for me but may be someone else out there as well. And who better to dedicate this creation to other than our ‘Heroes of hope’, the health care workers at the frontline who are fighting the pandemic day in and day out, without any selfish motives. Putting their lives at risk, away from their families, I can’t even begin to imagine the agony they must be going through.
Selected Entries in Science
Selected Entries in Art
Many thanks to everyone who participated.
Education Corner: Biomolecular Modeling in Elementary and Middle School
06/02/2020
The Spring 2020 issue of the RCSB PDB Newsletter is now online.
Award-Winning Videos on Molecular Mechanisms of Opioid Action
05/19/2020
High school students are excellent science communicators. The submitted entries in this year's Video Challenge demonstrate tremendous creativity and used many storytelling approaches to communicate the Molecular Mechanisms of Opioid Action.
Congratulations to the 2020 Prize Winners
- First Place: Saving Hector's Friend From Opioids by Elena Baraznenok from Bothell High School, Bothell, WA (Team advisor: Sheila Guard)
- Second Place: Fighting Opioids: One Punch at a Time by Naomi Yu, Janice Rateshwar, and Harrison Kane from Jericho High School, Jericho, NY (Team Advisor: Michael Giallorenzo)
- Third Place (tie): Opioidbusters by Radeha Haque, Christine Chung, Jenni Ren from The Bronx Highschool of Science, Bronx, NY (Team Advisor: Mr. Richard Lee)
- Third Place (tie): Visualizing Opioid Action at The Molecular Level: Through Drawn Animations by Minjune Song from Loomis Chaffee School, Windsor, CT (Team Advisor: Elliot Beck)
- Viewers’ Choice: The Opioid Crisis: Understanding the Mechanisms Behind this Deadly Epidemic by Arya Sasne and Mishal Shafique from West Windsor-Plainsboro High School South, West Windsor, NJ (Team Advisor: Matthew Foret)
Our panel of expert judges (Margaret A. Franzen (MSOE Center for BioMolecular Modeling), Steven W. Levison (New Jersey Medical School, Rutgers University), and Christine D. Young (University of Illinois at Chicago) scored the videos based on Quality of Storytelling (20%), Quality of Science Communication (30%), Quality of Public Health Message (10%), Originality and Creativity (20%), Quality of Production (10%), and Proper Accreditation (10%).
The general public voted for the Viewer's Choice Award.
Many thanks to the expert judges, students, teachers, parents, and voters who made this exciting competition happen!
Happy 70th Anniversary, National Science Foundation
05/10/2020
On May 10, 1950, Congress established the National Science Foundation to promote the progress of science, to advance the national health, prosperity, and welfare; and to secure the national defense. This year marks the 70th anniversary of NSF’s founding.

Credit: Nicolle R. Fuller, National Science Foundation
Milestone PDB structures are included on the NSF History Wall: HIV capsid (PDB structure 3j3q and #20 on Wall); green fluorescent protein (GFP), a powerful cellular biology research tool (PDB structure 1gfl and #26); and CRISPR, the enzyme revolutionizing biotech and health (PDB structure 4P6I and #61). #NSFstories
The NSF support for the RCSB PDB and PDB archive has been critical over the years. In return, RCSB PDB works with US Structural Biologists and users of the Cornell High Energy Synchrotron Source (CHESS) to enable research across all NSF directorates from agriculture to zoology.
RCSB PDB supports an international community of millions of users, including biologists (in fields such as structural biology, biochemistry, genetics, pharmacology); other research scientists (in fields such as bioinformatics); software developers for data analysis and visualization; students and educators (all levels); media writers, illustrators, textbook authors; and the general public.
RCSB PDB education efforts are built to broaden access and engagement with biomolecules. Features aimed at training the next generation of PDB users include the Molecule of the Month series, curricular materials and training guides, and individual research experiences for undergraduates.
RCSB PDB is supported by grants from the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198. In the past, RCSB PDB was also funded by the National Library of Medicine, the National Center for Research Resources, the National Institute of Biomedical Imaging and Bioengineering, and the National Institute of Neurological Disorders and Stroke.
Vote Now for the Viewer's Choice Award
05/05/2020
RCSB PDB challenged high school students to create short videos that tell stories about Molecular Mechanisms of Opioid Action.
Watch the challenge entries online and cast your vote for your favorite video by May 12.
Award winners will be announced on RCSB.org and PDB101.rcsb.org on May 19, 2019.
Coronavirus Background For Virtual Meetings
05/03/2020
Download images created by David Goodsell to add a molecular backdrop to your next virtual meeting.

June 1: Retirement of Protein Workshop and Ligand Explorer
05/01/2020
On June 1, 2020, Java-based tools Protein Workshop and Ligand Explorer will be retired. The 3D viewer Mol* has been updated to include features from these tools.
Mol* includes features such as viewing ligand environments; measuring distances within a structure; highlighting particular structural regions using the sequence display; changing the representation of particular residues; displaying symmetry related molecules; and displaying electron density maps.
Questions about Mol*? Share feedback using the "Contact Us" button on the right of any page.
Enter the Coronavirus CellPAINT Contest by May 31
04/28/2020
Show us how you can illustrate coronavirus with a new version of CellPAINT. The Scripps Research Center for Computational Structural Biology (CCSB) in association with RCSB PDB is hosting an image contest. There are two categories: Science and Art.
CellPAINT
CellPAINT is software for drawing pictures of cellular and viral systems, similar to a traditional digital paint program. The shapes and sizes of molecules are based on atomic structures taken from the Protein Data Bank, and the program allows you to build membranes, add membrane-bound proteins, and fill the inside and outside with soluble proteins and other molecules (more information).
For this contest, you can submit images created using the web-based program or the stand-alone version.
About the RCSB PDB and PDB-101
RCSB.org enables breakthroughs in scientific and biomedical research and education through tools and resources built on top of the PDB archive of 3D proteins and nucleic acids. Access COVID-19-related resources at the main RCSB PDB site and in the special section on Coronavirus at PDB-101, the educational portal of the RCSB PDB.
Contest Overview
- The contest is open to all, with one entry per person in each category.
- Submitted should be still images submitted in a familiar format (jpg, tiff, etc), that use CellPAINT in some or all of the image creation.
- The contest will be judged by members of the CCSB and RCSB PDB.
- Participants are encouraged to share their entries online with the hashtag #CVbyCellPAINT, but need to submit using the online form to be considered.
Submit by May 31, 2020:
Option 1: I have a Google Account
Option 2: I don't have a Google account
Use this form to register and then email images to RCSB PDB
Celebrate DNA Day on April 25
04/24/2020
DNA Day commemorates the completion of the Human Genome Project in 2003 and the discovery of DNA's double helix in 1953. Celebrate by:
- Creating a paper model of DNA (available in English and Spanish from PDB-101)
- Visiting the National Human Genome Research Institute's DNA Day website for teaching tools, chatroom, and webcasts
- Extracting DNA in your kitchen (strawberries recommended; you can pound them in a plastic bag instead of using the blender)
- Exploring Molecule of the Month features on DNA, Designed DNA Crystal, DNA Polymerase, and more at PDB-101

Annual Report Published
04/20/2020
Download the 2019 Annual Report (PDF) for an overview of recent Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education activities.
This review highlights many RCSB PDB accomplishments, including a look at recent COVID-19 developments, 20 years of Molecule of the Month, and the impact of the PDB archive on cancer drug approvals.
These bulletins provide a yearly snapshot of RCSB PDB activities and the state of the PDB archive.
Molecular Backgrounds For Virtual Meetings
04/07/2020
Download images created by David Goodsell to add a molecular backdrop to your next virtual meeting. Click on the image to expand.



Spring Newsletter Published
04/06/2020
The Spring 2020 issue of the RCSB PDB Newsletter is now online.
This issue highlights Enabling Structural Exploration of COVID-19; Beta testing of new features; Curated files for 3D printing; and more.
The Education Corner by Daniel Fried (Saint Peter’s University) describes Embedding Biomolecular Modeling in Elementary and Middle School Curriculum.
High School Students: Submit Opioid Action Videos Before April 28
03/31/2020
When used as prescribed by the physician, opioid drugs are very effective in treating moderate to severe pain. However, the misuse of these drugs has led to a spike in opioid addiction that is currently plaguing the nation. One of the ways to address opioid addition crisis is by improving patient awareness. Your video should tell a story that includes the molecular mechanism of opioid action that connects in some way to the current opioid crisis.
High school students can help increase awareness by participating in the 2020 Video Challenge for High School Students on Molecular Mechanisms of Opioid Action.
Submit your entry on or before April 28, 2020. Visit PDB-101 for contest details, resources, guidelines, and the panel of expert judges.
Beta Test the Next Generation RCSB.org
03/25/2020
Test drive significantly revised and updated tools for searching and exploring PDB data at beta.rcsb.org before this new site is moved into production later in April.
Improved and enhanced tools include:
- Basic Search available from the search box at the top of every page
- Advanced Search Boolean options
- Display of Advanced Search results for PDB structures, assemblies or unique polymeric molecular entities (unique sequences)
- Structure and Sequence Similarity and Annotation Browsing integration in Advanced Search
- Left-hand menu for refining Search Results
- Stored Search History
- New MyPDB features: registration via Google/Facebook/ORCID authentication; save/rerun/receive email notifications of searches
- Improved Download Tool for batches of data files
- New GraphQL and REST APIs for data access and searching
Please note some RCSB PDB features are still in development but will be made available soon, including Custom Tabular Reports and a Chemical Component Search tool.
Your feedback will help ensure RCSB PDB services support our users. Please use the orange Contact Us button on the middle of the right-hand side of each page.
Video: Fighting Coronavirus with Soap
03/23/2020

Coloring Coronavirus
03/17/2020

Brain Awareness Week
03/16/2020
Brain Awareness Week (BAW) is a nationwide effort organized by the Dana Alliance for Brain Initiatives and the Society for Neuroscience to promote the public and personal benefits of brain research. Molecule of the Month, now in its 20th year, offers resources to get started.
The brain orchestrates everything we do, sending signals through the nervous system to control different parts of our body. The brain is also the home of our thoughts and consciousness, as neurons process the input from our senses and store what they find as memories. Many drugs are available to help tune the function of the brain and nervous system when there are problems. Unfortunately, the effects of some drugs are hard to control and can lead to abuse and addiction. Explore PDB-101 Resources to learn about proteins related to our nervous system and mental health.
The theme for the 2020 Video Challenge for High School Students is Molecular Mechanisms of Opioid Action. Entries can be submitted until April 28, 11:59 pm PST. Award winners will be announced on May 19.
Curated Files for 3D Printing
03/06/2020
PDB-101 has launched a curated collection of files for 3D printing models of alpha-amylase, ferritin, GFP, and hemoglobin. Each 3D model file highlights a special feature of the molecule and its function. Suggested modeling additions, such as making heme molecules, can help tell a molecular story.
An overview is provided to start to create models for any PDB structure.
Please share any printed models with the team at info@rcsb.org, Facebook, or Twitter.
Education Corner: Using PDB in the College Classroom
02/19/2020
The Winter 2020 issue of the RCSB PDB Newsletter is now online.
Images from the Protein Data Bank (PDB) often appear in textbooks, flyers and posters—the colors and shapes are eye-catching and engaging for scientists and non-scientists alike. In the Education Corner, Bonnie Hall (Grand View University) describes how the initial interest in these images can be leveraged to engage students in a variety of chemistry classes in Using the Protein Data Bank in the College Classroom.
Molecular Landscapes: Coronavirus
02/15/2020
A new painting by David S. Goodsell depicts a coronavirus just entering the lungs, surrounded by mucus secreted by respiratory cells, secreted antibodies, and several small immune systems proteins. The image is available for download from the Molecular Landscapes SciArt Gallery.
This painting is accompanied by the February Molecule of the Month feature on Coronavirus Proteases. The article was inspired by the recent release of PDB structure 6lu7, a high-resolution crystal structure of COVID-19 coronavirus 3CL hydrolase (Mpro) as determined by Zihe Rao and Haitao Yang's research team at ShanghaiTech University.
Goodsell's molecular landscapes are available from PDB-101 in a special SciArt Digital Archive. These watercolor paintings integrate information from structural biology, microscopy and biophysics to simulate detailed views of the molecular structure of living cells. These illustrations are free for use under CC-BY-4.0 license. Acknowledgement should be given as indicated for each illustration.


Molecular Valentines
02/13/2020
COVID-19 Coronavirus Resources
02/06/2020
PDB data and related resources provide a starting point for structure-guided drug discovery and understanding of COVID-19.
- PDB structure 6lu7: first high-resolution crystal structure of COVID-19 coronavirus 3CL hydrolase (Mpro) determined by Zihe Rao and Haitao Yang's research team at ShanghaiTech University (released February 5, 2020). doi: 10.2210/pdb6lu7/pdb
- wwPDB overview, including summary data for closely-related PDB structures (96% sequence identity; CSV) and other closely related SARS proteins, including a second viral protease, the RNA polymerase, the viral spike protein, a viral RNA, and other proteins (CSV)
- Molecule of the Month feature on Coronavirus Proteases
- Coronavirus painting
Images
Coronavirus, 2020. Illustration by David S. Goodsell, RCSB Protein Data Bank doi: 10.2210/rcsb_pdb/goodsell-gallery-019
Download high quality TIFF image
COVID-19 coronavirus main protease, with inhibitor in turquoise. Image from the February 2020 Molecule of the Month article.
Download high quality TIFF image


PDB Structures: Access all 29 COVID19-related PDB structures

Zhenming Jin, Xiaoyu Du, Yechun Xu, Yongqiang Deng, Meiqin Liu, Yao Zhao, Bing Zhang, Xiaofeng Li, Leike Zhang, Chao Peng, Yinkai Duan, Jing Yu, Lin Wang, Kailin Yang, Fengjiang Liu, Rendi Jiang, Xinglou Yang, Tian You, Xiaoce Liu, Xiuna Yang, Fang Bai, Hong Liu, Xiang Liu, Luke W. Guddat, Wenqing Xu, Gengfu Xiao, Chengfeng Qin, Zhengli Shi, Hualiang Jiang, Zihe Rao, Haitao Yang
Structure of Mpro from COVID-19 virus and discovery of its inhibitors. bioRxiv
doi: 10.1101/2020.02.26.964882
PDB structure 6vsb doi: 10.2210/pdb6vsb/pdb D. Wrapp, N. Wang, K.S. Corbett, J.A. Goldsmith, C.-L. Hsieh, O. Abiona, B.S. Graham, J.S. McLellan (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Science doi: 10.1126/science.abb2507
Released 2020-02-26
Shown: Cryoelectron microscopy structure of 2019-nCoV (COVID-19) spike glycoprotein (PDB ID 6vsb) in the prefusion conformation, with the three subunits of the trimer in red, green, and blue, and glycosylation in yellow.
PDB structure 6lxt
Y. Zhu, F. Sun Structure of post fusion core of 2019-nCoV S2 subunit doi: 10.2210/pdb6lxt/pdb
Released 2020-02-26
PDB structure 6lvn
Y. Zhu, F. Sun Structure of the 2019-nCoV HR2 Domain doi: 10.2210/pdb6lvn/pdb
Released 2020-02-26
PDB structure 6vw1
J. Shang, G. Ye, K. Shi, Y.S. Wan, H. Aihara, F. Li Structural basis for receptor recognition by the novel coronavirus from Wuhan doi: 10.2210/pdb6vw1/pdb
Released 2020-03-04
PDB structure 6vww
Y. Kim, R. Jedrzejczak, N. Maltseva, M. Endres, A. Godzik, K. Michalska, A. Joachimiak, Center for Structural Genomics of Infectious Diseases Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 doi: 10.2210/pdb6vww/pdb
Released 2020-03-04
PDB structure 6y2e
L. Zhang, X. Sun, R. Hilgenfeld Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease doi: 10.2210/pdb6y2e/pdb
Released 2020-03-04
PDB structure 6y2f
L. Zhang, X. Sun, R. Hilgenfeld Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) doi: 10.2210/pdb6y2f/pdb
Released 2020-03-04
PDB structure 6y2g
L. Zhang, X. Sun, R. Hilgenfeld Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) doi: 10.2210/pdb6y2g/pdb
Released 2020-03-04
COVID-19 main protease with unliganded active site and PanDDA analysis Deposition Group: G_1002135 (8 structures)
PDB structure 6Y84
C.D. Owen, P. Lukacik, C.M. Strain-Damerell, A. Douangamath, A.J. Powell, D. Fearon, J. Brandao-Neto, A.D. Crawshaw, D. Aragao, M. Williams, R. Flaig, D. Hall, K. McAauley, D.I. Stuart, F. von Delft, M.A. Walsh
COVID-19 main protease with unliganded active site doi: 10.2210/pdb6y84/pdb
Released 2020-03-11
PDB structure 5R7Y
D. Fearon, A.J. Powell, A. Douangamath, C.D. Owen, C. Wild, T. Krojer, P. Lukacik, C.M. Strain-Damerell, M.A. Walsh, F. von Delft
Crystal Structure of COVID-19 main protease in complex with Z45617795 doi: 10.2210/pdb5r7y/pdb
Released 2020-03-11
PDB structure 5R7Z
D. Fearon, A.J. Powell, A. Douangamath, C.D. Owen, C. Wild, T. Krojer, P. Lukacik, C.M. Strain-Damerell, M.A. Walsh, F. von Delft
Crystal Structure of COVID-19 main protease in complex with Z1220452176 doi: 10.2210/pdb5r7z/pdb
Released 2020-03-11
PDB structure 5R80
D. Fearon, A.J. Powell, A. Douangamath, C.D. Owen, C. Wild, T. Krojer, P. Lukacik, C.M. Strain-Damerell, M.A. Walsh, F. von Delft
Crystal Structure of COVID-19 main protease in complex with Z18197050 doi: 10.2210/pdb5r80/pdb
Released 2020-03-11
PDB structure 5R81
D. Fearon, A.J. Powell, A. Douangamath, C.D. Owen, C. Wild, T. Krojer, P. Lukacik, C.M. Strain-Damerell, M.A. Walsh, F. von Delft
Crystal Structure of COVID-19 main protease in complex with Z1367324110 doi: 10.2210/pdb5r81/pdb
Released 2020-03-11
PDB structure 5R82
D. Fearon, A.J. Powell, A. Douangamath, C.D. Owen, C. Wild, T. Krojer, P. Lukacik, C.M. Strain-Damerell, M.A. Walsh, F. von Delft
Crystal Structure of COVID-19 main protease in complex with Z219104216 doi: 10.2210/pdb5r82/pdb
Released 2020-03-11
PDB structure 5R83
D. Fearon, A.J. Powell, A. Douangamath, C.D. Owen, C. Wild, T. Krojer, P. Lukacik, C.M. Strain-Damerell, M.A. Walsh, F. von Delft
Crystal Structure of COVID-19 main protease in complex with Z44592329 doi: 10.2210/pdb5r83/pdb
Released 2020-03-11
PDB structure 5R84
D. Fearon, A.J. Powell, A. Douangamath, C.D. Owen, C. Wild, T. Krojer, P. Lukacik, C.M. Strain-Damerell, M.A. Walsh, F. von Delft
Crystal Structure of COVID-19 main protease in complex with Z31792168 doi: 10.2210/pdb5r84/pdb
Released 2020-03-11
PDB structure 6vyb SARS-CoV-2 spike ectodomain structure (open state)
Alexandra C. Walls, Young-Jun Park, M. Alejandra Tortorici, Abigail Wall, Andrew T. McGuire, David Veesler (2020) Structure, Function, and Antigenicity of the SARSCoV-2 Spike Glycoprotein Cell 180: 1-12 doi: 10.1016/j.cell.2020.02.058
Released 2020-03-11
PDB structure 6vxx Structure of the SARS-CoV-2 spike glycoprotein (closed state)
Alexandra C. Walls, Young-Jun Park, M. Alejandra Tortorici, Abigail Wall, Andrew T. McGuire, David Veesler (2020) Structure, Function, and Antigenicity of the SARSCoV-2 Spike Glycoprotein Cell 180: 1-12 doi: 10.1016/j.cell.2020.02.058
Released 2020-03-11
PDB structure 6m17
Renhong Yan, Yuanyuan Zhang, Yaning Li, Lu Xia, Yingying Guo, Qiang Zhou (2020) Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2 Science doi: 10.1126/science.abb2762
Released 2020-03-11
SARS-CoV2 binds to the receptor protein ACE2 on the surface of cells that it infects. By studying the interaction of the SARS-CoV-2 spike protein (S) to this receptor, researchers hope to design new inhibitors to block infection. Several structures have recently been released that reveal this interaction. 6m17 is the structure of the receptor binding domain (RBD) of SARS-CoV-2 S protein with the ACE2-B^0 AT1 complex, suggesting simultaneous binding of two S protein trimers to an ACE2 dimer. 6m18 and 6m1d are ACE2-B^0 AT1 complex structures in closed and open forms without RBD binding. B^0 AT1 stabilizes full length ACE2 in the structural studies.
PDB structure 6vyo
C. Chang, K. Michalska, R. Jedrzejczak, N. Maltseva, M. Endres, A. Godzik, Y. Kim, A. Joachimiak Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2 doi: 10.2210/pdb6vyo/pdb
Released 2020-03-11
PDB structure 6w01
Y. Kim, R. Jedrzejczak, N. Maltseva, M. Endres, A. Godzik, K. Michalska, A. Joachimiak The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate doi: 10.2210/pdb6w01/pdb
Released 2020-03-11
PDB structure 6w02
K. Michalska, Y. Kim, R. Jedrzejczak, N. Maltseva, M. Endres, A. Mececar, A. Joachimiak Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose doi: 10.2210/pdb6w02/pdb
Released 2020-03-11
PDB structure 6m03
B.Zhang, Y. Zhao, Z. Jin, X. Liu, H. Yang, Z. Rao, The crystal structure of COVID-19 main protease in apo form doi: 10.2210/pdb6m03/pdb
Released 2020-03-11
Released 2020-03-18
- 6LZG: Q.H. Wang, H. Song, J.X. Qi, Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2 doi: 10.2210/pdb6lzg/pdb
- 6M0J: X. Wang, Crystal structure of 2019-nCoV spike receptor-binding domain bound with ACE2 doi: 10.2210/pdb6m0j/pdb
- 6M3M: S. Chen, S. Kang, Structural insights of SARS-CoV-2 nucleocapsid protein RNA binding domain reveal potential unique drug targeting sites doi: 10.2210/pdb6m3m/pdb
- 6W4B: K. Tan, Y. Kim, R. Jedrzejczak, N. Maltseva, M. Endres, K. Michalska, A. Joachimiak, CSGID, The crystal structure of Nsp9 replicase protein of COVID-19 doi: 10.2210/pdb6w4b/pdb
- 6W4H: G. Minasov, L. Shuvalova, M. Rosas-Lemus, O. Kiryukhina, G. Wiersum, A. Godzik, L. Jaroszewski, P.J. Stogios, T. Skarina, K.J.F. Satchell, 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2 doi: 10.2210/pdb6w4h/pdb
New Coronavirus Protease Structure Available
02/04/2020
PDB data provide a starting point for structure-guided drug discovery
A high-resolution crystal structure of COVID-19 (2019-nCoV) coronavirus 3CL hydrolase (Mpro) has been determined by Zihe Rao and Haitao Yang's research team at ShanghaiTech University. Rapid public release of this structure of the main protease of the virus (PDB 6lu7) will enable research on this newly-recognized human pathogen.
Recent emergence of the COVID-19 coronavirus has resulted in a WHO-declared public health emergency of international concern. Research efforts around the world are working towards establishing a greater understanding of this particular virus and developing treatments and vaccines to prevent further spread.
While PDB entry 6lu7 is currently the only public-domain 3D structure from this specific coronavirus, the PDB contains structures of the corresponding enzyme from other coronaviruses. The 2003 outbreak of the closely-related Severe Acute Respiratory Syndrome-related coronavirus (SARS) led to the first 3D structures, and today there are more than 200 PDB structures of SARS proteins. Structural information from these related proteins could be vital in furthering our understanding of coronaviruses and in discovery and development of new treatments and vaccines to contain the current outbreak.
The coronavirus 3CL hydrolase (Mpro) enzyme, also known as the main protease, is essential for proteolytic maturation of the virus. It is thought to be a promising target for discovery of small-molecule drugs that would inhibit cleavage of the viral polyprotein and prevent spread of the infection.
Comparison of the protein sequence of the COVID-19 coronavirus 3CL hydrolase (Mpro) against the PDB archive identified 95 PDB proteins with at least 90% sequence identity. Furthermore, these related protein structures contain approximately 30 distinct small molecule inhibitors, which could guide discovery of new drugs. Of particular significance for drug discovery is the very high amino acid sequence identity (96%) between the COVID-19 coronavirus 3CL hydrolase (Mpro) and the SARS virus main protease (PDB 1q2w). Summary data about these closely-related PDB structures are available (CSV) to help researchers more easily find this information. In addition, the PDB houses 3D structure data for more than 20 unique SARS proteins represented in more than 200 PDB structures, including a second viral protease, the RNA polymerase, the viral spike protein, a viral RNA, and other proteins (CSV).
Public release of the COVID-19 coronavirus 3CL hydrolase (Mpro), at a time when this information can prove most vital and valuable, highlights the importance of open and timely availability of scientific data. The wwPDB strives to ensure that 3D biological structure data remain freely accessible for all, while maintaining as comprehensive and accurate an archive as possible. We hope that this new structure, and those from related viruses, will help researchers and clinicians address the COVID-19 coronavirus global public health emergency.
2019 FASEB BioArt Winner
01/21/2020
An image of Measles Virus Proteins from PDB-101's Molecule of the Month was among the 2019 Winners of FASEB's BioArt Competition. This year’s winning graphics represent a wide range of biomedical research, from pink lettuce leaves to a blood clot of a mouse.
2020 will be a year-long celebration of 20 Years of Molecule of the Month.
Winter Newsletter Published
01/14/2020
The Winter 2020 issue of the RCSB PDB Newsletter is now online.
This issue highlights 20 years of Molecule of the Month stories; 2019 deposition and access statistics; a new GPCR paper model for download; and more.
Images from the Protein Data Bank (PDB) often appear in textbooks, flyers and posters—the colors and shapes are eye-catching and engaging for scientists and non-scientists alike. In the Education Corner, Bonnie Hall (Grand View University) describes how the initial interest in these images can be leveraged to engage students in a variety of chemistry classes in Using the Protein Data Bank in the College Classroom.
Molecule of the Month Newsletter
01/06/2020
Created and illustrated by David S. Goodsell (RCSB PDB-Rutgers and The Scripps Research Institute) since January 2000, the Molecule of the Month series tells stories about molecular structure and function, their diverse roles within living cells, and the growing connections between biology and nanotechnology. The growth and popularity of the column led to the development of the PDB-101 educational website. Molecule of the Month content has inspired readers around the world, and is a regular read for students and researchers alike. Columns are so compelling that they have been accessed nearly a million times in 2019.
To celebrate this milestone anniversary, Goodsell’s column for January 2020 offers a personal meditation on the growing revolution in structural biology that provides these amazing glimpses into biology.
The celebration continues all year long--the 2020 calendar highlights the top-accessed articles year after year, culminating in the highest-ranked articles Hemoglobin and Catalase.

Celebrating 20 Years of Molecule of the Month
01/02/2020
Since 2000, the RCSB PDB Molecule of the Month series has introduced millions of visitors to the shape and function of the 3D structures archived in the Protein Data Bank.
Created and illustrated by David S. Goodsell (RCSB PDB-Rutgers and The Scripps Research Institute), this feature tells stories about molecular structure and function, their diverse roles within living cells, and the growing connections between biology and nanotechnology. The growth and popularity of the column led to the development of the PDB-101 educational website. Molecule of the Month content has inspired readers around the world, and is a regular read for students and researchers alike. Columns are so compelling that they have been accessed nearly a million times in 2019.
To celebrate this milestone anniversary, Goodsell’s column for January 2020 offers a personal meditation on the growing revolution in structural biology that provides these amazing glimpses into biology.
The celebration continues all year long--the 2020 calendar highlights the top-accessed articles year after year, culminating in the highest-ranked articles Hemoglobin and Catalase.
Past news and events have been reported at the RCSB PDB website and past Newsletters.