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Protein cages & nanoparticles (PDB): 41 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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Encapsulin nanocompartment — Crystal structure of thermotoga maritima encapsulin — X-ray structure, 2008 (PDB 3DKT), downloaded from the RCSB Protein Data Bank.
Lumazine synthase cage — Synthase/riboflavin synthase complex of bacillus subtilis — X-ray structure, 1996 (PDB 1RVV), downloaded from the RCSB Protein Data Bank.
Designed protein nanoparticle — Structure of nanoparticle released from enveloped protein nanoparticle — cryo-EM structure, 2016 (PDB 5KP9), downloaded from the RCSB Protein Data Bank.
Small heat-shock protein cage — Small heat shock protein from methanococcus jannaschii — X-ray structure, 1999 (PDB 1SHS), downloaded from the RCSB Protein Data Bank.
Bacterioferritin — Iron storage and electron transport — X-ray structure, 1996 (PDB 1BFR), downloaded from the RCSB Protein Data Bank.
Pyruvate dehydrogenase E2 core — Dihydrolipoyl transacetylase (e.c.2.3.1.12) catalytic domain (residues 184-425) from bacillus stearothermophilus — X-ray structure, 1999 (PDB 1B5S), downloaded from the RCSB Protein Data Bank.
Vault particle — The structure of rat liver vault at 3.5 angstrom resolution — X-ray structure, 2014 (PDB 4V60), downloaded from the RCSB Protein Data Bank.
Ferritin cage — Human h chain ferritin — X-ray structure, 1997 (PDB 2FHA), downloaded from the RCSB Protein Data Bank.
Apoferritin (cryo-EM) — 1.25 a structure of human apoferritin obtained from titan mono-bcor microscope — cryo-EM structure, 2020 (PDB 6Z6U), downloaded from the RCSB Protein Data Bank.
Designed tetrahedral protein cage T33-21 — Computationally designed two-component self-assembling tetrahedral cage, t33-21, crystallized in space group r32 — X-ray structure, 2014 (PDB 4NWP), downloaded from the RCSB Protein Data Bank.
Lumazine synthase nucleocapsid (120-mer) — Aquifex aeolicus lumazine synthase-derived nucleocapsid variant nc-1 (120-mer) — cryo-EM structure, 2021 (PDB 7A4F), downloaded from the RCSB Protein Data Bank.
Designed icosahedral cage I53-40 — Crystal structure of designed two-component self-assembling icosahedral cage i53-40 — X-ray structure, 2016 (PDB 5IM5), downloaded from the RCSB Protein Data Bank.
De novo designed tetrahedral nanoparticle — De novo designed tetrahedral nanoparticle t33_dn10 — cryo-EM structure, 2020 (PDB 6VFH), downloaded from the RCSB Protein Data Bank.
Designed tetrahedral cage T33-31 — Crystal structure of rescued two-component self-assembling tetrahedral cage t33-31 — X-ray structure, 2015 (PDB 4ZK7), downloaded from the RCSB Protein Data Bank.
Designed icosahedral cage I32-28 — Crystal structure of designed two-component self-assembling icosahedral cage i32-28 — X-ray structure, 2016 (PDB 5IM6), downloaded from the RCSB Protein Data Bank.
HIV Env trimers on I53-50 nanoparticle (vaccine) — Bg505 sosip-i53-50np — cryo-EM structure, 2019 (PDB 6P6F), downloaded from the RCSB Protein Data Bank.
Designed octahedral cage O333 — Computationally designed self-assembling octahedral cage protein, o333, crystallized in space group r32 — X-ray structure, 2012 (PDB 3VCD), downloaded from the RCSB Protein Data Bank.
Dodecameric ferritin (Listeria Dps) — The x-ray structure of the unusual dodecameric ferritin from listeria innocua, reveals a novel intersubunit iron binding site. — X-ray structure, 2000 (PDB 1QGH), downloaded from the RCSB Protein Data Bank.
Dps — Structural studies of n terminal deletion mutant of dps from mycobacterium smegmatis — X-ray structure, 2007 (PDB 2YW6), downloaded from the RCSB Protein Data Bank.
Dps — The crystal structure of dps, a ferritin homolog that binds and protects dna — X-ray structure, 1998 (PDB 1DPS), downloaded from the RCSB Protein Data Bank.
Dps (DNA-protecting protein) — Dna protection and binding by e. coli dps protein — X-ray structure, 2003 (PDB 1JTS), downloaded from the RCSB Protein Data Bank.
Encapsulin (T. maritima) — Myxococcus xanthus encapsulin protein (enca) — cryo-EM structure, 2014 (PDB 4PT2), downloaded from the RCSB Protein Data Bank.
Encapsulin T=4 — Cryo-em structure of a thermostable encapsulin from t. maritima — cryo-EM structure, 2021 (PDB 7KQ5), downloaded from the RCSB Protein Data Bank.
Encapsulin — Encapsulin iron storage compartment from quasibacillus thermotolerans — cryo-EM structure, 2019 (PDB 6NJ8), downloaded from the RCSB Protein Data Bank.
Carboxysome CcmK — Carboxysome protein csos1a from halothiobacillus neapolitanus — X-ray structure, 2006 (PDB 2EWH), downloaded from the RCSB Protein Data Bank.
Carboxysome shell protein CcmK2 — Ccmk2 - form 1 dodecamer — X-ray structure, 2012 (PDB 3SSQ), downloaded from the RCSB Protein Data Bank.
BMC shell — Structure of the intact haliangium ochraceum microcompartment shell — X-ray structure, 2017 (PDB 5V74), downloaded from the RCSB Protein Data Bank.
BMC shell — Cryo-em structure of the ho bmc shell: icosahedral reconstruction (main population) — cryo-EM structure, 2019 (PDB 6MZX), downloaded from the RCSB Protein Data Bank.
Small heat-shock protein assemblies — Multiple distinct assemblies reveal conformational flexibility in the small heat shock protein hsp26 — cryo-EM structure, 2006 (PDB 2H53), downloaded from the RCSB Protein Data Bank.
Polyhedrin crystal — The crystal structure of infectious cypovirus polyhedra — X-ray structure, 2007 (PDB 2OH5), downloaded from the RCSB Protein Data Bank.
Vault — Re-refinement of the vault ribonucleoprotein particle — X-ray structure, 2013 (PDB 4HL8), downloaded from the RCSB Protein Data Bank.
GroEL–GroES — Crystal structure of groel-groes — X-ray structure, 2003 (PDB 1PCQ), downloaded from the RCSB Protein Data Bank.
GroEL — Groel using cryoem — cryo-EM structure, 2017 (PDB 5W0S), downloaded from the RCSB Protein Data Bank.
GroEL–GroES chaperonin — Crystal structure of groel14-groes7-(adp-alfx)7 — X-ray structure, 2005 (PDB 1SVT), downloaded from the RCSB Protein Data Bank.
TRiC chaperonin — Crystal structure of the chaperonin from thermococcus strain ks-1 (two-point mutant complexed with amp-pnp) — X-ray structure, 2004 (PDB 1Q3Q), downloaded from the RCSB Protein Data Bank.
TRiC/CCT chaperonin — The crystal structures of the eukaryotic chaperonin cct reveal its functional partitioning — X-ray structure, 2014 (PDB 4V8R), downloaded from the RCSB Protein Data Bank.
GroEL (apo) — A 3.02 angstrom crystal structure of wild-type apo groel in a monoclinic space group — X-ray structure, 2007 (PDB 2NWC), downloaded from the RCSB Protein Data Bank.
Proteasome (archaeal) — Proteasome from thermoplasma acidophilum — X-ray structure, 1996 (PDB 1PMA), downloaded from the RCSB Protein Data Bank.
HslUV protease–chaperone — Crystal structure of the hsluv protease-chaperone complex — X-ray structure, 2000 (PDB 1G3I), downloaded from the RCSB Protein Data Bank.
20S proteasome (mouse) — Mouse constitutive 20s proteasome — X-ray structure, 2012 (PDB 3UNE), downloaded from the RCSB Protein Data Bank.
E2 core — Atomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex — X-ray structure, 1993 (PDB 1EAA), downloaded from the RCSB Protein Data Bank.