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
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.
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.
Illustration by David S. Goodsell, RCSB Protein Data Bank doi: 10.2210/rcsb_pdb/goodsell-gallery-019
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
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
Color an image (PDF) of coronavirus based on a painting by David S. Goodsell.
Video: Fighting Coronavirus with Soap and related imagesPDB Structures: Access all 29 COVID19-related PDB structures
PDB structure 6lu7 Released 2020-02-05Zhenming 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.
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.
