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Hemoglobin
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A pan-hantavirus neutralizing antibody, called ADI-65534 (blue) binds to the interface between Gc and Gn envelope proteins (pdb_00009p3y and pdb_00007qqb). Only the antigen-binding region of the antibody is shown in this structure, and the transmembrane domains of the envelope proteins are not shown.
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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.
Still image from 3D animation depicting the maturation step of the Human Immunodeficiency Virus life cycle.
"The march of progress" graphic created using miniproteins
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.
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.
2 "lego" researchers at a table in front of a screen that reads "OneDep". A "lego" Krios Cryo-TEM is in the background
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.
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.
Impact of PDB Structures on US FDA Anti-Cancer Drug Approvals (2010-2023)
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.
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.
Cats Iris (tortoise) and Ares (grey) on a Molecular Landscape painting of Lipid Droplets
Screenshot of online game
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Anakin Padme 4 Panel Meme: 1 Structures in PDB format 2 Do you mean mmCIF and not deprecated format, right 3 4 Right?
3DEM Model-Map percentile slider from the wwPDB validation report
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).
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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.
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Hand holding paper model of HIV capsid
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.
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).
Workshop attendees
"Let's align our coordinates" valentine with Oxytocin receptor ("love hormone") aligned with vasopressin receptor
Valentine that reads "All is FAIR in love and data"
Collage of images related to James Andrew Harris from Waco History https://wacohistory.org/items/show/197
GOLLD RNA complexes have been solved as 10-subunit (top left, pdb_00009lee), 12-subunit (right, pdb_00009l0r), and 14-subunit (bottom left, pdb_00009mee) structures.
Cover Image Description from Journal: Contemporary vaccine design relies on iterative, rational engineering to sculpt immunogens capable of eliciting protective immune responses. When the correct shape is formed and each fine line expertly carved, repeated copies of the immunogen can be produced to inspire immune protection. In the July issue of Trends in Immunology, Li et al. trace the evolution of rationally designed Lassa virus glycoproteins and present a novel immunogen template, illustrated through the linoleum prints, as a promising step toward next-generation vaccines that elicit previously unattainable, but protective neutralizing responses against lethal Lassa virus infection. Image credit: Woodcut art and photo by Sigrid Knemeyer.
Collage of PDB structures on the covers of journals
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OLE RNA from Clostridium botulinum (pdb_00009lcr) is shown in pink on the left. ROOL RNAs can form cages built from 6 (right, top, pdb_00009j6y) or 8 (right, bottom, pdb_00009mds) subunits.
Photo collage of RCSB PDB meetings and celebrations
Credit: Nucleic Acids Research (2025). DOI: 10.1093/nar/gkaf1029
A nanoscale box made by DNA origami.
Images from PDB-101 videos showing (clockwise from upper left) X-ray crystallography, NMR, and 3DEM
FOXP3 forkhead box domains (green) can polymerize and bring together multiple strands of DNA (purple and blue). PDB 9D2L shows how four strands of DNA can be linked by FOXP3.
Brian
The GLP-1 receptor, which is a member of a large class of G protein-coupled receptors, undergoes a series of conformational changes when it is activated. In the absence of an agonist, the extracellular domain of the receptor is closed and interacts with the transmembrane domain (PDB 6LN2). On the intracellular side, the structure is tightly packed, stabilized by interactions between amino acids in different alpha helices. Upon binding GLP-1 (shown in pink on the right, PDB 6X18), the extracellular domain moves up to accommodate the ligand, which also causes an opening on the intracellular side of the receptor. This allows the binding and activation of a G protein (not shown), which in turn pushes one of the receptor’s transmembrane helices outward. The result is a disruption of stabilizing contacts within the receptor and the initiation of downstream signaling that influences appetite and metabolism.
Osteocalcin (blue) is essential for both bone growth and the development of bone strength. Within bone tissue, it forms bonds with the surface of calcium-containing crystals called hydroxyapatite by interacting with three calcium ions (yellow). Through these ionic bonds, osteocalcin can fine-tune the alignment of hydroxyapatite crystals to ensure they are parallel to collagen fibrils. This arrangement reinforces bone strength in the direction where they are subjected to significant stresses. Illustration by RCSB PDB intern Xinyi Christine Zhang.
PDB Cake!
On the left, GLP-1 binds to the GLP-1 receptor, which itself is bound to a trimeric G protein (PDB 6B3J). On the right, GIP binding to a G protein-bound GIP receptor is shown (PDB 7RA3).
Examples of ABA created in Jsmol
Cover of American Scientist September-October 2025 Volume: 113 Number: 5 When HIV enters a cell, its genome (white strand, top right corner) incorporates into the cell’s genome in the nucleus. As the cell activates its genes, the virus’s genes turn on too. The cell then transcribes the viral RNA (yellow squiggles), which moves through the cell and is used to synthesize the virus’s proteins (red). As the viral RNA and proteins accumulate at the cell’s membrane, the immature viral particles bud off, taking with them pieces of the membrane and its proteins (magenta). Viral enzymes finish processing the proteins to create the HIV capsid (the protein shell that encloses the virus’s genome) leading to a fully mature virus particle. (Cover illustration by David S. Goodsell, B-HIVE Center, RCSB Protein Data Bank and Scripps Research. doi:10.2210/rcsb_pdb/goodsell-gallery-047)
The natural protein RcoM
Vitamin A plays a crucial role in vision by converting light into electrical signals. At the heart of this process are rhodopsin proteins (purple) found in the retina, a light-sensing tissue at the back of the eye. Vitamin A is the precursor to retinal (yellow), which is nestled within the active site of rhodopsin. When light strikes retinal, it transforms from its cis form to its trans form (see inset), allowing rhodopsin to bind and activate its associated G-protein complex (green). This process sets off a cascade of events that ultimately leads to the perception of light. Visit the 2025 Calendar: The Structural Biology of Nutrition to learn more. Illustration by RCSB PDB intern Xinyi Christine Zhang.
A comparison of the structures of dArc1 (capsid: 6TAP; pentamer: 6TAR), the retrovirus HIV (capsid: 3J3Q; pentamer: 7URN), and the retrotransposon Ty3 (6R24). Pentamers are shown in orange, and hexamers in yellow in the upper panel. In the lower panel, pentamers are shown with monomers colored in different shades of orange.
DECTRIS (logo) detecting the future
Team members and students in front of a collagen sculpture
Playing card featuring Rosalind Franklin
Fatty acids are essential for energy storage and are vital components of various tissues. Fatty Acid Synthase (FAS) is the master architect behind the construction of these fats. FAS is a sophisticated enzymatic system comprising two identical protein subunits, each folded into seven interconnected functional domains. It functions like an assembly line, with each domain catalyzing a distinct step in the reaction and with the growing fatty acid chain being transferred from one active site to the next. These active sites are marked with bright flashes. Visit the 2025 Calendar: The Structural Biology of Nutrition to learn more. Illustration by RCSB PDB intern Xinyi Christine Zhang.