Spring Newsletter Published

04/13/2021

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The Spring 2021 issue of the RCSB PDB Newsletter is now online.

This issue highlights PDB50 anniversary celebrations; the CellPAINT contest (submit images by May 1); new search tools; and more.

The Education Corner by RCSB PDB's Maria Voigt Explores the Structure-Function Relationship with Digital and Physical 3D Models of Proteins.

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Developers: HTTPS enforcement starts May 10

04/09/2021

RCSB PDB APIs, RCSB.org, and PDB101.rcsb.org will enforce use of the secure HTTPS protocol starting May 10, 2021. HTTP Strict Transport Security headers will be implemented.

RCSB.org data and services have supported supported HTTPS protocol since 2017, but with this change all users will be redirected to HTTPS to guarantee secure communication.

Programmatic users are encouraged to switch to HTTPS as soon as possible. Not all HTTP clients will necessarily follow redirects automatically.

Individual website users should not be impacted, as modern web browsers will redirect automatically.

Download Molecular Landscapes

04/06/2021

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

Painting of a portrait of SARS-CoV-2 March-April, 2021

This 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. The virus is shown in magenta, and the droplet is also filled with molecules that are present in the respiratory tract, including mucins (green), pulmonary surfactant proteins and lipids (blue), and antibodies (tan). The painting was created as part of the show New Ways of Living with SciCommMake.

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.

Enter the 2021 CellPAINT Contest by May 1

04/01/2021

Show us illustrations inspired by vaccines and by 50 years of the PDB 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 of Vaccines and 50 Years of PDB.

Images for the Science of Vaccines category need to be accurate and present aspects of structure and biology--create something that helps us understand vaccines and how they work.

In the 50 Years of PDB category, let your creativity run wild with any topic that celebrates 50 years of access to biological macromolecules in the Protein Data Bank archive--create something that amazes and inspires.

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.

Information about new molecules added to CellPAINT for drawing illustrations of mRNA vaccines like the ones being used to fight COVID-19 is available.

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 hashtags #VaccinesByCellPAINT or #CelebratePDB, but need to submit using the online form to be considered.

Submit by May 1, 2021

Winners of each category will be awarded:

A set of PDB-themed cards created by David S. Goodsell.

Waived admission to the inaugural event: A special virtual symposium celebrating the 50th anniversary of the Protein Data Bank (May 4-5, 2021) (new registrations only).

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).

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. RCSB PDB and the wwPDB are celebrating the 50th Anniversary of the PDB with symposia, materials, and more.

Molecular Landscapes: E. coli

03/23/2021

A new painting by David S. Goodsell illustrates a cross-section through an Escherichia coli cell. The image is available for download from the Molecular Landscapes SciArt Gallery.

This painting is an update of an earlier E. coli painting from 1999, incorporating abundant new data that has been gathered since then, including proteomics information and many amazing new structures.

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-028

Submit Abstracts for PDB50

03/07/2021

Throughout 2021, RCSB PDB and the wwPDB will celebrate the 50th anniversary of the PDB archive (wwpdb.org/pdb50 and wwpdb.org/pdb50).

The inaugural symposium will be held virtually on May 4-5, 2021.

The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day. The event will be recorded and made available to registered participants after the meeting.

Students and postdoctoral fellows are especially encouraged to attend and will be eligible for poster awards.

Abstract submission and reduced registration rates end March 15.
Register at https://www.asbmb.org/meetings-events/pdb50.

Speakers

More than 1,000 SARS-CoV-2 Coronavirus Protein Structures Available

03/02/2021

With this week's update, 1,018 SARS-CoV-2-related structures are now freely available from the Protein Data Bank.

The first SARS-CoV-2 structure, a high-resolution crystal structure of the coronavirus main protease (PDB 6lu7), was released early in the pandemic on February 5, 2020.

Since then, structural biologists have visualized most of the SARS-CoV-2 proteome, including the spike protein binding to its ACE2 receptor and neutralizing antibodies, and the main protease, the papain-like proteinase, and other promising drug discovery targets. All of the structures and related data are available for exploration from wwPDB partner websites: RCSB PDB, PDBe, PDBj, and BMRB.

Rapid public release of SARS-CoV-2 structure data has greatly increased our understanding of Covid-19, allowed direct visualization of emerging variants of the virus, and facilitated structure-guided drug discovery and reuse to combat infection. Open access to PDB structures has already enabled design of effective vaccines against SARS-CoV-2.

The response of the research community to the pandemic has highlighted the importance of open access to scientific data in real time. 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.

The impact of these 1018 structures and many more coronavirus protein structures to come stands as a testament to the importance of open access to structural biology research data.

Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-024.
Visit PDB-101 for related educational materials.

High School Students: Submit Videos By April 27

02/25/2021

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. Sometimes this input is not processed right. This can be modulated by the drugs prescribed by the doctors to amplify or to soften the neuronal signal.

High school students can help increase awareness by participating in the 2021 Video Challenge for High School Students on Molecular Mechanisms of Drugs for Mental Disorders.

Submit your entry on or before April 27, 2021. Visit PDB-101 for contest details, resources, guidelines, and the panel of expert judges.

Join Us at the Feb 24 Biophysical Society Job Fair

02/21/2021

Meet with team members to learn about open positions for Scientific Software Developers (Rutgers and UCSD), Postdoctoral Researchers (UCSD), and summer undergraduate researchers (virtually at Rutgers).

RCSB PDB is a world-renowned, scientific organization focused on serving technical, educational and other programmatic needs of scientific and research communities worldwide. RCSB.org serves millions of users in academia and industry. The RCSB PDB development team, located at UCSD/SDSC and Rutgers, creates leading edge web technologies targeted for scientific and educational audiences.

Join the RCSB PDB and participate in exciting projects with significant impact on the scientific community.

Can't attend the fair? Please Contact Us with any questions.

RCSB PDB Team in 2020

PDB50: Submit Posters by March 15

02/15/2021

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive.

The inaugural symposium will be held May 4-5, 2021 in an event hosted by the American Society for Biochemistry and Molecular Biology and organized by the wwPDB Foundation.

This celebration of the 50th anniversary of the founding of the Protein Data Bank as the first open access digital data resource in biology will include presentations from speakers from around the world who have made tremendous advances in structural biology and bioinformatics.

Attendees are encouraged to participate in the virtual poster session and exhibition hall. Students and postdoctoral fellows will be eligible for poster awards.

Register and submit abstracts by March 15th, 2021 for reduced rates.

Speakers will include:

• Edward Arnold - Rutgers, The State University of New Jersey
• Helen M. Berman - Rutgers, The State University of New Jersey and University of Southern California
• Thomas L. Blundell - University of Cambridge
• Alexandre M. J. J. Bonvin - Utrecht University
• Stephen K. Burley - Rutgers, The State University of New Jersey and University of California San Diego
• Wah Chiu - Stanford University
• Johann Deisenhofer - University of Texas Southwestern Medical Center
• Juli Feigon - University of California Los Angeles
• Angela M. Gronenborn - University of Pittsburgh
• Jennifer L. Martin - University of Wollongong
• Stephen L. Mayo - California Institute of Technology
• Zihe Rao - ShanghaiTech University and Tsinghua University
• Hao Wu - Boston Children's Hospital and Harvard Medical School

The online sessions will take place between 11 a.m. – 4:30 p.m. EST each day. The event will be recorded and made available to registered participants after the meeting.

Sponsorship opportunities are available; please contact the wwPDB Foundation for more information.

Molecular Valentines

02/11/2021

Click on each image to expand.

Tribute to Rosalind Franklin

Atomic structures are being used to design effective vaccines against SARS-CoV-2

Antibodies are our molecular watchdogs, waiting and watching for viruses, bacteria and other unwelcome visitors.

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)