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Protein design & nanocages (PDB): 72 3D models

DNA, RNA, nucleic-acid drugs, gene editing, proteins and 300+ real PDB structures (real sizes 1–100 nm). Each one is a ready-made 3D model you can turn, recolour and place in a figure — open BioDioRama and type its name in the Library search.

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Octameric de novo designed peptide — Octameric de novo designed peptide — X-ray structure, 2002 (PDB 1L4X), downloaded from the RCSB Protein Data Bank.
Symfoil-4T Permutation #3: de novo designed beta-trefoil… — Crystal structure of symfoil-4t permutation #3: de novo designed beta-trefoil architecture with symmetric primary structure — X-ray structure, 2011 (PDB 3P6J), downloaded from the RCSB Protein Data Bank.
De novo designed ferredoxin-ferredoxin domain insertion protein — Crystal structure of de novo designed ferredoxin-ferredoxin domain insertion protein — X-ray structure, 2015 (PDB 5CW9), downloaded from the RCSB Protein Data Bank.
De novo designed miniprotein Gpx15 in the P 42 21 2 space group — Crystal structure of the de novo designed miniprotein gpx15 in the p 42 21 2 space group. — X-ray structure, 2026 (PDB 27AG), downloaded from the RCSB Protein Data Bank.
De novo designed voltage-gated anion channel (dVGAC) — Cryo-em structure of a de novo designed voltage-gated anion channel (dvgac) — Cryo-EM structure, 2025 (PDB 8YQ6), downloaded from the RCSB Protein Data Bank.
De novo designed exatecan-binding protein, EPIC Q51N — De novo designed exatecan-binding protein, epic q51n — X-ray structure, 2026 (PDB 9NZG), downloaded from the RCSB Protein Data Bank.
16 nm protein cage designed by fusing symmetric oligomeric domains — Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains — X-ray structure, 2012 (PDB 3VDX), downloaded from the RCSB Protein Data Bank.
C2 symmetric interface of designed zinc-induced tetrahedron… (9K8C) — Cryo-em structure of c2 symmetric interface of designed zinc-induced tetrahedron cage-t32-zn1-hehe-34 — Cryo-EM structure, 2025 (PDB 9K8C), downloaded from the RCSB Protein Data Bank.
Monomer of designed zinc-induced tetrahedron Cage-t32-Zn1-HEHE-35 — Cryo-em structure of monomer of designed zinc-induced tetrahedron cage-t32-zn1-hehe-35 — Cryo-EM structure, 2025 (PDB 9K8F), downloaded from the RCSB Protein Data Bank.
C2 symmetric interface of designed zinc-induced tetrahedron… (9K8H) — Cryo-em structure of c2 symmetric interface of designed zinc-induced tetrahedron cage-t32-zn1-hehe-35 — Cryo-EM structure, 2025 (PDB 9K8H), downloaded from the RCSB Protein Data Bank.
Monomer of designed zinc-induced tetrahedron Cage-t32-Zn1-HEHE-36 — Cryo-em structure of monomer of designed zinc-induced tetrahedron cage-t32-zn1-hehe-36 — Cryo-EM structure, 2025 (PDB 9K8J), downloaded from the RCSB Protein Data Bank.
C2 symmetric interface of designed zinc-induced tetrahedron… (9K8K) — Cryo-em structure of c2 symmetric interface of designed zinc-induced tetrahedron cage-t32-zn1-hehe-36 — Cryo-EM structure, 2025 (PDB 9K8K), downloaded from the RCSB Protein Data Bank.
C3 symmetric interface of designed zinc-induced tetrahedron… (9K8L) — Cryo-em structure of c3 symmetric interface of designed zinc-induced tetrahedron cage-t32-zn1-hehe-36 — Cryo-EM structure, 2025 (PDB 9K8L), downloaded from the RCSB Protein Data Bank.
Encapsulin from Dendrosporobacter quercicolus — Structure of encapsulin from dendrosporobacter quercicolus — Cryo-EM structure, 2025 (PDB 9I8E), downloaded from the RCSB Protein Data Bank.
Klebsiella pneumoniae DyP peroxidase-loaded encapsulin shell — Klebsiella pneumoniae dyp peroxidase-loaded encapsulin shell — Cryo-EM structure, 2024 (PDB 8U50), downloaded from the RCSB Protein Data Bank.
Single particle reconstruction of Rhodospirillum rubrum encapsulin — Single particle reconstruction of rhodospirillum rubrum encapsulin — Cryo-EM structure, 2026 (PDB 9RY4), downloaded from the RCSB Protein Data Bank.
Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore… — Cargo-loaded myxococcus xanthus enca encapsulin engineered pore mutant with t=4 icosahedral symmetry — Cryo-EM structure, 2024 (PDB 9BC8), downloaded from the RCSB Protein Data Bank.
Heterologous protein complex loaded Thermotoga maritima encapsulin… — Cryo-em structure of heterologous protein complex loaded thermotoga maritima encapsulin capsid — Cryo-EM structure, 2020 (PDB 7K5W), downloaded from the RCSB Protein Data Bank.
Focused refinement of closed pentamer of the Rhodospirillum rubrum… — Focused refinement of closed pentamer of the rhodospirillum rubrum encapsulin from symmetry expansion of icosahedral single particle reconstruction — Cryo-EM structure, 2026 (PDB 9RY7), downloaded from the RCSB Protein Data Bank.
Pentameric fungal and an icosahedral plant lumazine synthase reveals… (1C2Y) — Crystal structures of a pentameric fungal and an icosahedral plant lumazine synthase reveals the structural basis for differences in assembly — X-ray structure, 2000 (PDB 1C2Y), downloaded from the RCSB Protein Data Bank.
Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05… — Crystal structure of lumazine synthase from brucella abortus (orthorhombic form at 3.05 angstroms) — X-ray structure, 2005 (PDB 1XN1), downloaded from the RCSB Protein Data Bank.
3D Structure of Lumazine Synthase from Candida albicans — 3d structure of lumazine synthase from candida albicans — X-ray structure, 2007 (PDB 2JFB), downloaded from the RCSB Protein Data Bank.
Pentameric fungal and an icosahedral plant lumazine synthase reveals… (1C41) — Crystal structures of a pentameric fungal and an icosahedral plant lumazine synthase reveals the structural basis for differences in assembly — X-ray structure, 2000 (PDB 1C41), downloaded from the RCSB Protein Data Bank.
Recombinant Lumazine synthase (hexagonal form) — Recombinant lumazine synthase (hexagonal form) — X-ray structure, 2006 (PDB 1ZIS), downloaded from the RCSB Protein Data Bank.
Aquifex aeolicus lumazine synthase 11-pentamer cage — Aquifex aeolicus lumazine synthase 11-pentamer cage — Cryo-EM structure, 2026 (PDB 9RYO), downloaded from the RCSB Protein Data Bank.
Aquifex aeolicus lumazine synthase R29A mutant 11-pentamer cage — Aquifex aeolicus lumazine synthase r29a mutant 11-pentamer cage — Cryo-EM structure, 2026 (PDB 9RYQ), downloaded from the RCSB Protein Data Bank.
Aquifex aeolicus lumazine synthase L121A mutant 11-pentamer cage — Aquifex aeolicus lumazine synthase l121a mutant 11-pentamer cage — Cryo-EM structure, 2026 (PDB 9RYV), downloaded from the RCSB Protein Data Bank.
Aquifex aeolicus lumazine synthase I125A mutant 11-pentamer cage — Aquifex aeolicus lumazine synthase i125a mutant 11-pentamer cage — Cryo-EM structure, 2026 (PDB 9RYX), downloaded from the RCSB Protein Data Bank.
PLL9 induced TmFtn nanocage — Pll9 induced tmftn nanocage — X-ray structure, 2022 (PDB 7VVS), downloaded from the RCSB Protein Data Bank.
Ferritin nanocage containing Au and Pt, obtained upon encapsulation… (6FX8) — The x-ray structure of the ferritin nanocage containing au and pt, obtained upon encapsulation of a single heterobimetallic compound within the protein cage (rotating anode data) — X-ray structure, 2018 (PDB 6FX8), downloaded from the RCSB Protein Data Bank.
Enhancing the Gastric Stability of Ferritin Nanocage via… — Enhancing the gastric stability of ferritin nanocage via computational-assisted disulfide bond engineering — X-ray structure, 2025 (PDB 8YKR), downloaded from the RCSB Protein Data Bank.
Horse spleen apoferritin (control) — X-ray structure of horse spleen apoferritin (control) — X-ray structure, 2016 (PDB 5ERK), downloaded from the RCSB Protein Data Bank.
DiRu-1-encapsulated Apoferritin — X-ray structure of diru-1-encapsulated apoferritin — X-ray structure, 2019 (PDB 6GXJ), downloaded from the RCSB Protein Data Bank.
Marsupenaeus japonicus ferritin mutant-D132R — Marsupenaeus japonicus ferritin mutant-d132r — X-ray structure, 2021 (PDB 7DQO), downloaded from the RCSB Protein Data Bank.
De novo designed miniprotein binder against PDL1, Gpx41 — Crystal structure of the de novo designed miniprotein binder against pdl1, gpx41. — X-ray structure, 2026 (PDB 27RQ), downloaded from the RCSB Protein Data Bank.
De novo designed serotonin binder SROb2_26_L7F — Crystal structure of de novo designed serotonin binder srob2_26_l7f — X-ray structure, 2026 (PDB 9V3A), downloaded from the RCSB Protein Data Bank.
De novo designed serotonin binder SROb2_30 — Crystal structure of de novo designed serotonin binder srob2_30 — X-ray structure, 2026 (PDB 9V39), downloaded from the RCSB Protein Data Bank.
X-ray crystal structure of a de novo designed lumiflavin binder… — X-ray crystal structure of a de novo designed lumiflavin binder, sc-apcc-4-lmf-1 — X-ray structure, 2026 (PDB 9R1M), downloaded from the RCSB Protein Data Bank.
X-ray crystal structure of a de novo designed Arcyriaflavin A… — X-ray crystal structure of a de novo designed arcyriaflavin a binder, sc-apcc-4-a7f-1 — X-ray structure, 2026 (PDB 9R1K), downloaded from the RCSB Protein Data Bank.
C3 symmetric interface of designed zinc-induced tetrahedron… (9K8G) — Cryo-em structure of c3 symmetric interface of designed zinc-induced tetrahedron cage-t32-zn1-hehe-35 — Cryo-EM structure, 2025 (PDB 9K8G), downloaded from the RCSB Protein Data Bank.
C3 symmetric interface of designed zinc-induced tetrahedron… (9K8D) — Cryo-em structure of c3 symmetric interface of designed zinc-induced tetrahedron cage-t32-zn1-hehe-34 — Cryo-EM structure, 2025 (PDB 9K8D), downloaded from the RCSB Protein Data Bank.
Encapsulin from Dendrosporobacter quercicolus, mutant N198W — Structure of encapsulin from dendrosporobacter quercicolus, mutant n198w — Cryo-EM structure, 2025 (PDB 9I8F), downloaded from the RCSB Protein Data Bank.
Encapsulin from Arthrobacter sp — Structure of encapsulin from arthrobacter sp. — Cryo-EM structure, 2025 (PDB 9I8D), downloaded from the RCSB Protein Data Bank.
Engineered Encapsulin P3P4 — Engineered encapsulin p3p4 — Cryo-EM structure, 2024 (PDB 8RVJ), downloaded from the RCSB Protein Data Bank.
De novo designed protein — de novo designed protein — X-ray structure, 2023 (PDB 8JU8), downloaded from the RCSB Protein Data Bank.
Ferritin nanocage assembly with nickel ion — ferritin nanocage assembly with nickel ion — X-ray structure, 2023 (PDB 7XRG), downloaded from the RCSB Protein Data Bank.
Ferritin nanocage containing Au and Pt, obtained upon encapsulation… (6FX9) — The x-ray structure of the ferritin nanocage containing au and pt, obtained upon encapsulation of a single heterobimetallic compound within the protein cage (synchrtron data) — X-ray structure, 2018 (PDB 6FX9), downloaded from the RCSB Protein Data Bank.
Auoxo3-encapsulated horse spleen apoferritin — X-ray structure of auoxo3-encapsulated horse spleen apoferritin — X-ray structure, 2016 (PDB 5IX6), downloaded from the RCSB Protein Data Bank.
De novo designed miniprotein Gpx15 in the C121 space group — Crystal structure of the de novo designed miniprotein gpx15 in the c121 space group. — X-ray structure, 2026 (PDB 27AH), downloaded from the RCSB Protein Data Bank.
De novo designed protein with buried polar network — De novo designed protein with buried polar network — X-ray structure, 2026 (PDB 13JM), downloaded from the RCSB Protein Data Bank.
De novo design of binder (#313) to monomeric Cu/Zn-superoxide dismutase — De novo design of binder (#313) to monomeric cu/zn-superoxide dismutase — X-ray structure, 2026 (PDB 23WS), downloaded from the RCSB Protein Data Bank.
X-ray crystal structure of a de novo designed SN38 binder… — X-ray crystal structure of a de novo designed sn38 binder, sc-apcc-4-sn38-1 — X-ray structure, 2026 (PDB 9R1L), downloaded from the RCSB Protein Data Bank.
De novo design of binder (#13136) to monomeric Cu/Zn-superoxide… — De novo design of binder (#13136) to monomeric cu/zn-superoxide dismutase — X-ray structure, 2026 (PDB 23WT), downloaded from the RCSB Protein Data Bank.
Capsid structure of the Syngnathus scovelli chapparvovirus… — Capsid structure of the syngnathus scovelli chapparvovirus virus-like particle — Cryo-EM structure, 2025 (PDB 9NEK), downloaded from the RCSB Protein Data Bank.
Recombinant Alfalfa Mosaic virus coat protein virus-like particle… — Recombinant alfalfa mosaic virus coat protein virus-like particle (ramv-cp vlp) — Cryo-EM structure, 2021 (PDB 7EPP), downloaded from the RCSB Protein Data Bank.
PT=3 virus-like particle of ssRNA phage Hubei14 coat protein — pt=3 virus-like particle of ssrna phage hubei14 coat protein — Cryo-EM structure, 2024 (PDB 9HAU), downloaded from the RCSB Protein Data Bank.
Virus-like particle of Beihai levi-like virus 14 — Virus-like particle of beihai levi-like virus 14 — X-ray structure, 2020 (PDB 6YFD), downloaded from the RCSB Protein Data Bank.
TTMV-LY1 anellovirus virus-like particle expressed in HEK293 — Cryo-em structure of ttmv-ly1 anellovirus virus-like particle expressed in hek293 — Cryo-EM structure, 2024 (PDB 8V7X), downloaded from the RCSB Protein Data Bank.
Virus-like particle from Pyrococcus furiosus — Crystal structure of virus-like particle from pyrococcus furiosus — X-ray structure, 2007 (PDB 2E0Z), downloaded from the RCSB Protein Data Bank.
Self-assembling galactosylated peptide homodimer — Crystal structure of a self-assembling galactosylated peptide homodimer — X-ray structure, 2020 (PDB 7C0N), downloaded from the RCSB Protein Data Bank.
Hexagonally Ordered Nanofibrils Easily Yield by dual Amphiphilic… — Hexagonally ordered nanofibrils easily yield by dual amphiphilic self-assembling peptide — Cryo-EM structure, 2026 (PDB 9H7U), downloaded from the RCSB Protein Data Bank.
Lipopeptide Detergent (LPD-12) — Crystal structure of lipopeptide detergent (lpd-12) — X-ray structure, 2008 (PDB 3CAY), downloaded from the RCSB Protein Data Bank.
Cyclic residues in alpha/beta-peptide helix bundles: GCN4-pLI side… (3HEV) — Cyclic residues in alpha/beta-peptide helix bundles: gcn4-pli side chain sequence on an (alpha-alpha-beta) backbone with a cyclic beta-residue at position 19 — X-ray structure, 2010 (PDB 3HEV), downloaded from the RCSB Protein Data Bank.
Cyclic residues in alpha/beta-peptide helix bundles: GCN4-pLI side… (3HEW) — Cyclic residues in alpha/beta-peptide helix bundles: gcn4-pli side chain sequence on an (alpha-alpha-beta) backbone with a cyclic beta-residue at position 22 — X-ray structure, 2010 (PDB 3HEW), downloaded from the RCSB Protein Data Bank.
Cyclic residues in alpha/beta-peptide helix bundles: GCN4-pLI side… (3HEX) — Cyclic residues in alpha/beta-peptide helix bundles: gcn4-pli side chain sequence on an (alpha-alpha-beta) backbone with cyclic beta-residues at positions 1, 4, 19 and 28 — X-ray structure, 2010 (PDB 3HEX), downloaded from the RCSB Protein Data Bank.
Cyclic residues in alpha/beta-peptide helix bundles: GCN4-pLI side… (3HET) — Cyclic residues in alpha/beta-peptide helix bundles: gcn4-pli side chain sequence on an (alpha-alpha-beta) backbone with a cyclic beta-residue at position 10 — X-ray structure, 2010 (PDB 3HET), downloaded from the RCSB Protein Data Bank.
Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic… — Polygalacturonate lyase by fusing with a self-assembling amphipathic peptide — X-ray structure, 2018 (PDB 5X2I), downloaded from the RCSB Protein Data Bank.
X-ray crystal structure of a de novo designed 1,6-diphenylhexatriene… — X-ray crystal structure of a de novo designed 1,6-diphenylhexatriene and nile red binder, sc-apcc-6-dph-nr — X-ray structure, 2026 (PDB 9R1O), downloaded from the RCSB Protein Data Bank.
PT=3 virus-like particle of ssRNA phage Beihai26 coat protein — pt=3 virus-like particle of ssrna phage beihai26 coat protein — Cryo-EM structure, 2024 (PDB 9HAT), downloaded from the RCSB Protein Data Bank.
PT=3 virus-like particle of ssRNA phage ESO003 coat protein — pt=3 virus-like particle of ssrna phage eso003 coat protein — Cryo-EM structure, 2024 (PDB 9HAS), downloaded from the RCSB Protein Data Bank.
Insight into Three-dimensional structure of Maize Chlorotic Mottle… — Insight into three-dimensional structure of maize chlorotic mottle virus revealed by single particle analysis — Cryo-EM structure, 2016 (PDB 3JB8), downloaded from the RCSB Protein Data Bank.
Cyclic residues in alpha/beta-peptide helix bundles: GCN4-pLI side… (3HEU) — Cyclic residues in alpha/beta-peptide helix bundles: gcn4-pli side chain sequence on an (alpha-alpha-beta) backbone with a cyclic beta-residue at position 13 — X-ray structure, 2010 (PDB 3HEU), downloaded from the RCSB Protein Data Bank.