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 the COVID-19 coronavirus.
- PDB structure 6lu7: high-resolution crystal structure of COVID-19 coronavirus 3CL hydrolase (Mpro) determined by Zihe Rao and Haitao Yang's research team at ShanghaiTech University. 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
Coronavirus, 2020. Illustration by David S. Goodsell, RCSB Protein Data Bank doi: 10.2210/rcsb_pdb/goodsell-gallery-019Download high quality TIFF image
PDB structure 6lu7 X. Liu, B. Zhang, Z. Jin, H. Yang, Z. Rao, The crystal structure of 2019-nCoV main protease in complex with an inhibitor N3.
doi: 10.2210/pdb6lu7/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.
