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.

The 2019 Nobel Prize for Physiology or Medicine was awarded to three researchers who discovered the molecular details of this central oxygen-sensing process, termed the HIF (Hypoxia-Inducible Factor) system.

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.

Takahiro Yamauchi

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)

Ravi Yadav

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.

All poster prize awardees will be listed on the RCSB PDB website and will receive an educational book.

Aya Narunsky

Respiratory Droplet

09/15/2020

Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-024

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 will receive a $250 cash prize sponsored by the Society of Physics Students and MiTeGen, as well as a gift certificate for MiTeGen products.

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

Acknowledgement: David S. Goodsell, RCSB Protein Data Bank and Springer Nature; doi: 10.2210/rcsb_pdb/goodsell-gallery-025

Volume 584 Issue 7821, 20 August 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

Chemical structures of remdesivir and its triphosphate product are shown at the top, and the drug is shown in red in the complex with RNA and the RNA-dependent RNA polymerase at the bottom.

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

Coronavirus Life Cycle by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-023
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.

Readers can also subscribe to a new electronic newsletter that will send alerts when new Molecule of the Month features are available.

(2020) BAMBed 48: 350-355 doi: 10.1002/bmb.21360

Summer Newsletter Published

07/28/2020

Sign up to receive electronic updates each quarter.

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

SARS-CoV-II spike protein (left) and a close-up of the interaction of the spike receptor binding domain with an antibody Fab.

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

A new publication identifies highly-cited PDB structures overall and in Materials Science, Physics, Computer Science, Chemistry, Engineering, and Mathematics to explore how PDB data are used across scientific fields.

Natalie Verdiguel and Zukang Feng at the 2018 RISE at Rutgers Symposium

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.

Nuclesome, potassium channel, and bacteriorhodopsin

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.

The PDB-101 portal promotes online exploration of proteins and nucleic acids for teachers, students, and the general public.

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.

The biocuration team described the privilege and responsibility of being a biocurator in a recent news article.

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.

Detail of the Coronavirus Life Cycle, 2020, by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-023

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

How SARS-CoV-2 interacts with the surface proteins of the target cell by Marta Palma Rodríguez (Graduate Student, Hospital General Universitario de Valencia).

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

Heroes of hope (Kanika Khanna, Stanford University)

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.

1. The central figure of the creation is a masked healthcare worker and all the components that make up the worker are molecules in our body that fight viral and bacterial infections, antibodies and components of complement system, namely IgA, IgG, IgM and Complement factors C3, H, C4A and B represented in the face, mask, neck and body of the worker. This is to represent that just as our body uses these molecules to fight an infection, the health care worker is fighting the deadly pandemic for the entire world and he/she may be our ‘antibody’ against the virus, so to say.
2. The mask also has actin which is known to have a rare combination of strength and sensitivity, being used in some of the most demanding structural activities in the body. This also represents the importance of wearing masks in these times not only to protect ourselves from the virus but others around us. I have also put a few ACE2 receptors embedded in the mask to show that these can be ‘buried’ or protected from viral infection with the proper use of face masks.
3. The virus particles shown on the outside have their nucleocapsid proteins arranged in symbol of ‘theta’, which is the Greek symbol of death representing the fatal powers of the virus. I am hoping with this creation, I am able to reach out to a broader audience with two messages. As the title of the creation ‘Heroes of hope’ suggests, we need to thank our healthcare workers big time for the contributions they are making to fight the deadly pandemic. Second, we need to be more vigilant about how we conduct ourselves so that we can keep each other safe during these tough times. Only then can we hope for a better future for the world today!

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

Sign up to receive electronic updates each quarter.

The Spring 2020 issue of the RCSB PDB Newsletter is now online.

In the Education Corner, Daniel Fried (St. Peter's University) describes describes his program Biochemistry Literacy for Kids. This digital curriculum helps kids easily gain a deep understanding of biology and chemistry to fast-track them to college-level learning.

Other articles in this issue highlight Enabling Structural Exploration of COVID-19; Beta testing of new features; Curated files for 3D printing; and more

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.

Caption: NSF History Wall, Alexandria, VA
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.

Voting is open through May 12.

Coronavirus Background For Virtual Meetings

05/03/2020

Download images created by David Goodsell to add a molecular backdrop to your next virtual meeting.

Coronavirus main protease virtual meeting background for download; based on PDB structure 6lu7

Other backgrounds are available for download from PDB-101

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.

Test drive using Mol* to view hemoglobin

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.

Images for the “Science” category need to be accurate and present aspects of coronavirus structure and biology--create something that helps us understand the virus.

In the “Art” category, let your creativity run wild with any topic--create something that amazes and inspires.

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.

A CellPAINT tutorial provides information on how to create images using the program and a summary of the ultrastructure of the virus.

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:

Winners of each category will be awarded an original painting by David S. Goodsell.

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

DNA and RNA are the cell’s way of storing and deploying genetic information. Structural biology is revealing that some nucleic acids also fold to form complex molecular machines. Guided by these structures, nanotech scientists are building new machines composed of nucleic acid. Learn 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.

Bacteriophage portal protein (PDB structure 5jj3)

Myoglobin (PDB structure 1mbn)

Crystal of DNA (PDB structure 167D)

Crystal of amyloid fibrils (PDB structure 2on9)

Crystal of nucleosome array (PDB structure 6hkt)

Crystal of HIV-1 capsid (PDB structure 6ay9)

Crystal of ferritin (PDB structure 2fg8)

Spring Newsletter Published

04/06/2020

Sign up to receive electronic updates each quarter.

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
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New Advanced Search Query Builder

Video: Fighting Coronavirus with Soap

03/23/2020

Always use soap when you wash your hands! Soap molecules break up the outer layer of enveloped viruses, stopping infection. Watch at the molecular level how soap breaks up coronavirus by using series of hydrophilic and hydrophobic interactions.

Coloring Coronavirus

03/17/2020

Color an image of coronavirus based on a painting by David S. Goodsell. The painting is available for download from the Molecular Landscapes SciArt Gallery.

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.

Acetylcholinesterase stops the signal between a nerve cell and a muscle cell

Adrenaline stimulates a G-protein-coupled receptor, priming us for action

Cell-clogging amyloids form when proteins improperly aggregate

Neurotrophins guide the development of the nervous system

Serotonin receptors control mood, emotion, and many other behaviors, and are targets for many important drugs

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

Sign up to receive electronic updates each quarter.

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.

Other articles in this issue highlight 20 years of Molecule of the Month stories; 2019 deposition and access statistics; a new GPCR paper model for download; and more.

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.

Illustration by David S. Goodsell, RCSB Protein Data Bank doi: 10.2210/rcsb_pdb/goodsell-gallery-019

PDB data provide a starting point for structure-guided drug discovery

The Molecule of the Month series is celebrating 20 years of sharing molecular stories about PDB structures.

Readers can subscribe to a new electronic newsletter that will send alerts when new Molecule of the Month features are available.

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.

Molecular Valentines

02/13/2020

DNA is composed of a long linear strand of millions of nucleotides, and is most often found paired with a partner strand

Organisms from fireflies to bacteria use luciferase to emit light

Concanavalin A and Circular Permutation: For some proteins, clipped and reassembled sequences can produce the same 3D shape

Oxytocin has been called the "love hormone" (more at Scientific American)

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

Color an image (PDF) of coronavirus based on a painting by David S. Goodsell.

Video: Fighting Coronavirus with Soap and related images

PDB Structures: Access all 29 COVID19-related PDB structures

PDB structure 6lu7 Released 2020-02-05
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

COVID-19 main protease protein with inhibitor N3 (white stick representation) covalently bound to residue cysteine 145 in the protease active site. Display shows secondary structure (helices in magenta, strands in cyan, loops in yellow). Adjacent active site residue histidine 41 is also shown.

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 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 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.

https://doi.org/10.2210/pdb6lu7/pdb

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

Sign up to receive electronic updates each quarter.

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

Subscribe to a new electronic newsletter that will send alerts when new Molecule of the Month features are available.

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.

The cover image, which highlights a Cross-Section of the Measles Virus, was recently selected as a winning entry in the FASEB BioArt Scientific Image and Video Competition.

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.

The cover image, which highlights a Cross-Section of the Measles Virus, was recently selected as a winning entry in the FASEB BioArt Scientific Image and Video Competition.

Readers can also subscribe to a new electronic newsletter that will send alerts when new features are available.

Download the calendar as a PDF, PowerPoint, or set of image files.