RCSB Protein Data Bank

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RCSB Protein Data Bank@rcsbpdb· 22d

Big PDB Changes Are One Year Away! On July 21, 2027, wwPDB will fully transition to extended PDB IDs for new depositions and the PDB archive will use a new directory structure based on 12-character extended PDB IDs. Visit wwpdb.org for details.

Be an Early Adopter:
Transition to the new PDB Beta Archive,
Extended PDB IDs, and PDBx/mmCIF File Format

The PDB Beta Archive contains all current PDB data and is updated weekly. Visit wwPDB.org for details.

RCSB Protein Data Bank@rcsbpdb· 25d

On the cover of Cell Genomics: The image depicts a nerine flower and the spatial structure of the VDAC protein, which the program NERINE links with Parkinson's disease. Artist: Rauf Sunyaev. www.cell.com/xgen/is...

On the cover: Nazeen et al. present NERINE, an algorithm used to study gene networks. The image depicts a nerine flower and the spatial structure of the VDAC protein, which the program NERINE links with Parkinson's disease. Artist: Rauf Sunyaev.

RCSB Protein Data Bank@rcsbpdb· Jul 7

The evolving landscape of molecular visualization Review traces the evolution of molecular visualization and explores how emerging technologies promise to make visualization not only a medium of communication but also a tool for scientific exploration onlinelibrary.wiley....

Still image from 3D animation depicting the maturation step of the Human Immunodeficiency Virus life cycle.

RCSB Protein Data Bank@rcsbpdb· Jul 4

Love this graphical abstract for "The Ascent of Miniproteins" pubs.acs.org/doi/ful...

"The march of progress" graphic created using miniproteins

RCSB Protein Data Bank@rcsbpdb· Jul 2

Athletes carb load to build up glycogen for heavy exertion, like the World Cup. When we eat lots of carbs, insulin (yellow) directs cells to gather glucose and store as glycogen (purple). When glucose is needed, glycogen phosphorylase releases glucose for energy production.

Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank. doi: 10.2210/rcsb_pdb/goodsell-gallery-014

This painting shows the binding of insulin (yellow) to insulin receptors and the processes that are triggered. It was created as part of the yearly focus on diabetes at PDB-101. The painting is featured in the Insulin and Diabetes poster that illustrates how structural biology has revealed the details of insulin signaling and how this knowledge is being used to create new and better treatments for diabetes.

RCSB Protein Data Bank@rcsbpdb· Jun 19

June 19 is World Sickle Cell Day. Sickle cell anemia is caused by change of a single glutamate to a valine in hemoglobin, which makes the protein prone to aggregation into long filaments. Image of Hemoglobin S by Irving Geis.

Geis illustrates the hemoglobin s molecule as four nearly symmetrically arranged subunits with a mutation present in the beta chain.

Used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved.

RCSB Protein Data Bank@rcsbpdb· Jun 16

Only a few slots left for the wwPDB workshops at #IUCr2027 ! Join us in Calgary to learn how to deposit with OneDep and/or PDB-IHM in FREE pre-conference events IUCr2026 www.wwpdb.org/news/n...

2 "lego" researchers at a table in front of a screen that reads "OneDep". A "lego" Krios Cryo-TEM is in the background

RCSB Protein Data Bank@rcsbpdb· Jun 12

Scientists are actively researching ways to make phage therapies more effective. This includes efforts to engineer phages to expand their host range and aid in bacterial defense system evasion. More at Molecule of the Month: pdb101.rcsb.org/motm...

Left: JBD30 is a siphophage that infects Pseudomonas aeruginosa by attaching to hair-like pili on the bacterial surface. This illustration was created by combining pdb_00008rkc, pdb_00008rkb, pdb_00008rk9, pdb_00008rk8, pdb_00008rk7, pdb_00008rk6,pdb_00008rk5, and pdb_00008rk4. Right: Andhra is a podophage that infects Staphylococcus epidermidis. This illustration was created by combining pdb_00008egt, pdb_00008egs, pdb_00008egr, and pdb_00008ej5.

RCSB Protein Data Bank@rcsbpdb· Jun 5

Myoglobin Fold (1987) by Irving Geis Used with permission from the Howard Hughes Medical Institute. All rights reserved. Learn more about Irving Geis and his his iconic images of DNA, hemoglobin, and other important macromolecules at PDB-101 pdb101.rcsb.org/sci-...

Geis illustrated the structure of myoglobin, focusing on the folding pattern of the secondary structure of the protein. Unlike previous myoglobin Illustrations, this painting focuses on the tertiary structure of the molecule rather than the sequence or surface.

RCSB Protein Data Bank@rcsbpdb· May 27

Impact of PDB Structures on Anti-Cancer Drug Approvals: Open access to PDB data facilitates discovery and development of life saving drugs Full flyer at cdn.rcsb.org/rcsb-pd... #NationalCancerResearchMonth

Impact of PDB Structures on US FDA Anti-Cancer Drug Approvals (2010-2023)

RCSB Protein Data Bank@rcsbpdb· May 25

Transglutaminases play essential roles in most of our cells, and also indispensable tools in food biotechnology. For example, a small bacterial transglutaminase helps improve the texture of hot dogs and other meat products #HappyMemorialDayWeekend pdb101.rcsb.org/motm...

Tissue transglutaminase in the active (left) and GTP-bound inactive (right) conformations. An inhibitor that mimics gluten is shown in yellow and GTP is shown in red.

RCSB Protein Data Bank@rcsbpdb· May 22

PROTACs: A modular approach to protein destruction More at Molecule of the Month: pdb101.rcsb.org/motm...

The PROTAC MZ1 (yellow, also shown in stick representation) brings together a target protein, BRD4 (pink), and the Von Hippel-Lindau E3 ligase (blue). Illustration created using pdb_00005t35 and pdb_00005n4w.

RCSB Protein Data Bank@rcsbpdb· May 21

May is National Pet Month. Cats Iris (tortoise) and Ares (grey) help RCSB PDB's Ezra Peisach manage the PDBx/mmCIF Dictionary and preparations for the upcoming transition to extended PDB IDs and the new Beta Archive www.rcsb.org/news/fe...

Cats Iris (tortoise) and Ares (grey) on a Molecular Landscape painting of Lipid Droplets

RCSB Protein Data Bank@rcsbpdb· May 16

Try this new online training game from Leandro F. Estrozi designed for newcomers in structural biology, with a focus on cryo-EM and cryo-ET map interpretation: rico.ibs.fr/helixplo...

RCSB Protein Data Bank@rcsbpdb· May 5

Today is the ABRCMS Day of Giving -- help support the scientists shaping tomorrow by visiting abrcms.org/donate/

Donate today to ABRCMS to help continue the conference

RCSB Protein Data Bank@rcsbpdb· May 4

Register for the June 1 Office Hour on Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF This Office Hour is for all users, but particularly for software developers and journal editors. Details: pdb101.rcsb.org/news...

Anakin Padme 4 Panel Meme:
1 Structures in PDB format
2 Do you mean mmCIF and not deprecated format, right
3
4 Right?

RCSB Protein Data Bank@rcsbpdb· Apr 23

wwPDB News: Updated Validation Reports for Released PDB and EMDB Entries Percentiles have been recalculated across the archive and reflect EDS and MolProbity updates, new Q-score percentile information for 3DEM entries, and ligand validation improvements. www.rcsb.org/news/fe...

3DEM Model-Map percentile slider from the wwPDB validation report

RCSB Protein Data Bank@rcsbpdb· Apr 21

The OR5 channel opens upon binding a variety of odorant molecules, including eugenol (orange) and DEET (green) More at April's Molecule of the Month: pdb101.rcsb.org/motm...

Odorant receptors from the jumping bristletail form homotetramers made up of four identical OR subunits. The OR5 channel, shown above (pdb_00007lic), opens upon binding a variety of odorant molecules, including eugenol (orange, pdb_00007lid) and DEET (green, pdb_00007lig).

RCSB Protein Data Bank@rcsbpdb· Apr 9

RCSB PDB has launched a chatbot to answer general questions about structure deposition, biocuration, validation or PDB policies. Try it today and rate the response: rcsb-deposit-help.rc...

RCSB Protein Data Bank@rcsbpdb· Apr 7

RCSB PDB wants to learn how users are utilizing integrative (IHM) structures and Computed Structure Models (CSMs) at RCSB PDB. Please take this brief survey: go.rutgers.edu/pqz9bucz Respondents can enter into a drawing for a canvas featuring the artwork of David S. Goodsell.

Take the survey to win a 4 x 6" canvas of Insulin Release, 2022 by David S. Goodsell.

RCSB Protein Data Bank@rcsbpdb· Mar 13

PDB-101 Focus: Biotechnology Learn how researchers are using biology in industry. Learn how GFP-like proteins found in nature or engineered in the laboratory now span every color of the rainbow pdb101.rcsb.org/motm...

Sampler of the fluorescent proteins that are currently available in the PDB archive (3m24 , 2q57 , 4ar7 , 2y0g , 1huy , 2h5o , 2h5q ). All of these proteins are similar to GFP, with the familiar beta barrel fold surrounding a self-assembled chromophore threaded through the center of the molecule. The variously colored chromophores, however, differ slightly from one another and the amino acids surrounding the chromophore further tune the light that is emitted.

RCSB Protein Data Bank@rcsbpdb· Mar 10

Last few #ASBMB2026 #ASBMB26 hours -- come visit RCSB PDB in the exhibit hall and poster session. Not at the meeting? Take the PDB-101 User Survey and Win Share your feedback and enter into a drawing for a Molecule of the Month-themed sticker set at rutgers.ca1.qualtric...

Take the survey to win stickers of images from Molecule of the Month and the Molecular Landscapes gallery of David S. Goodsell paintings.
Clockwise, from upper left: Chloroplast, Red fluorescent protein, Measles Virus Proteins, Myoglobin in a Whale Muscle Cell.

RCSB Protein Data Bank@rcsbpdb· Mar 8

Build a paper model of the HIV capsid using this template from PDB-101 #ASBMB2026 #ASBMB26 pdb101.rcsb.org/lear...

RCSB Protein Data Bank@rcsbpdb· Mar 8

Researchers found that treatment of intact HIV capsids with lenacapavir causes capsids to rupture, with ruptures occurring first in areas of the capsid with the highest level of curvature. #ASBMB2026 #ASBMB26 Watch in 3D at PDB-101: pdb101.rcsb.org/motm...

Structural studies have provided new insights into lenacapavir's unique mechanism of action. Using electron cryotomography, researchers found that treatment of intact HIV capsids with lenacapavir causes capsids to rupture, with ruptures occurring first in areas of the capsid with the highest level of curvature. The walls of lenacapavir-treated capsids were observed to flatten during early time points and fragment over the course of the experiment. This process is shown in the animation, created by Rachel Torrez in collaboration with Owen Pornillos (University of Utah). The animation was created using pdb_00009pry and pdb_00009y7j and their corresponding models in the EM Data Bank, EMD-71816 and EMD-72657.

RCSB Protein Data Bank@rcsbpdb· Feb 16

Surprisingly, histones have also been characterized in bacteria, including a bacterium found in soil and aquatic environments and in a spiral-shaped gram-negative bacterium More at Molecule of the Month: pdb101.rcsb.org/motm...

Bacterial histone assemblies from Bdellovibrio bacteriovorus (purple, end-on binding mode from pdb_00008fw7 and pdb_00009ezz shown in middle row, and center-binding mode from pdb_00009f0e shown in bottom row) and Leptospira perolatii (pink, pdb_00009qt1 and pdb_00009qt2).

RCSB Protein Data Bank@rcsbpdb· Feb 14

Building the Future of Structural Biology in Africa Through Training and Partnership from Protein Society mailchi.mp/proteinso...

RCSB Protein Data Bank@rcsbpdb· Feb 10

Use RCSB PDB's Pairwise Structure Alignment tool to compare existing PDB structures or Computed Structure Models (or upload a local file) #LoveDataWeek www.rcsb.org/alignment

"Let's align our coordinates" valentine with Oxytocin receptor ("love hormone") aligned with vasopressin receptor

RCSB Protein Data Bank@rcsbpdb· Feb 9

Happy #LoveDataWeek ! Celebrate with World Data System and their Feb 10 webinar "Persistent Identifiers: Enabling Trust & Discovery in Research Data" Details: ow.ly/XCrT50Y0ABG

Valentine that reads "All is FAIR in love and data"

RCSB Protein Data Bank@rcsbpdb· Feb 7

Today is Periodic Table Day Read about James Andrew Harris and the discovery of rutherfordium dubnium #BlackHistoryMonth wacohistory.org/item... chemistry.berkeley.e...

Collage of images related to James Andrew Harris from Waco History https://wacohistory.org/items/show/197

RCSB Protein Data Bank@rcsbpdb· Jan 27

Given the hollow cage-like structures of ROOL and GOLLD complexes, researchers suggest that they may act as structural scaffolds within the cell, helping to sequester or compartmentalize cellular components. More at Molecule of the Month: pdb101.rcsb.org/motm...