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Viral proteins & capsids (PDB): 96 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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RSV F bound to nirsevimab (MEDI8897) — Crystal structure of rsv f a2 bound to medi8897 — X-ray structure, 2017 (PDB 5UDC), downloaded from the RCSB Protein Data Bank.
Influenza HA with broadly neutralising antibody — Crystal structure of broadly neutralizing antibody cr8043 bound to h3 influenza hemagglutinin — X-ray structure, 2013 (PDB 4NM8), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike (closed) — Structure of the sars-cov-2 spike glycoprotein (closed state) — cryo-EM structure, 2020 (PDB 6VXX), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike (one RBD up) — Sars-cov-2 spike ectodomain structure (open state) — cryo-EM structure, 2020 (PDB 6VYB), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike (prefusion, vaccine design) — Prefusion 2019-ncov spike glycoprotein with a single receptor-binding domain up — cryo-EM structure, 2020 (PDB 6VSB), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 RBD bound to ACE2 — Crystal structure of sars-cov-2 spike receptor-binding domain bound with ace2 — X-ray structure, 2020 (PDB 6M0J), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 main protease — The crystal structure of covid-19 main protease in complex with an inhibitor n3 — X-ray structure, 2020 (PDB 6LU7), downloaded from the RCSB Protein Data Bank.
ACE2 receptor — Native human angiotensin converting enzyme-related carboxypeptidase (ace2) — X-ray structure, 2004 (PDB 1R42), downloaded from the RCSB Protein Data Bank.
1918 influenza hemagglutinin — 1918 h1 hemagglutinin — X-ray structure, 2004 (PDB 1RUZ), downloaded from the RCSB Protein Data Bank.
Influenza neuraminidase N1 — N1 neuraminidase — X-ray structure, 2006 (PDB 2HTY), downloaded from the RCSB Protein Data Bank.
Influenza neuraminidase N2 — Three-dimensional structure of the neuraminidase of influenza virus a(slash)tokyo(slash)3(slash)67 at 2.2 angstroms resolution — X-ray structure, 1992 (PDB 1NN2), downloaded from the RCSB Protein Data Bank.
Influenza M2 proton channel — Proton channel m2 from influenza a in complex with inhibitor rimantadine — NMR structure, 2008 (PDB 2RLF), downloaded from the RCSB Protein Data Bank.
Ebola virus glycoprotein — Crystal structure of the trimeric prefusion ebola virus glycoprotein in complex with a neutralizing antibody from a human survivor — X-ray structure, 2008 (PDB 3CSY), downloaded from the RCSB Protein Data Bank.
HIV-1 Env trimer (BG505 SOSIP) — Crystal structure of the bg505 sosip gp140 hiv-1 env trimer in complex with the broadly neutralizing fab pgt122 — X-ray structure, 2013 (PDB 4NCO), downloaded from the RCSB Protein Data Bank.
HIV gp120 bound to CD4 — Hiv-1 gp120 core complexed with cd4 and a neutralizing human antibody — X-ray structure, 1998 (PDB 1GC1), downloaded from the RCSB Protein Data Bank.
HIV-1 protease — Crystal structure at 1.9 angstroms resolution of human immunodeficiency virus (hiv) ii protease complexed with l-735,524, an orally bioav… — X-ray structure, 1996 (PDB 1HSG), downloaded from the RCSB Protein Data Bank.
HIV-1 reverse transcriptase with DNA — Structure of a catalytic complex of hiv-1 reverse transcriptase: implications for nucleoside analog drug resistance — X-ray structure, 1998 (PDB 1RTD), downloaded from the RCSB Protein Data Bank.
HIV-1 capsid protein hexamer — X-ray structure of hexameric hiv-1 ca — X-ray structure, 2009 (PDB 3H47), downloaded from the RCSB Protein Data Bank.
RSV fusion protein (prefusion) — Crystal structure of respiratory syncytial virus fusion glycoprotein stabilized in the prefusion conformation by human antibody d25 — X-ray structure, 2013 (PDB 4JHW), downloaded from the RCSB Protein Data Bank.
Zika virus — The cryo-em structure of zika virus — cryo-EM structure, 2016 (PDB 5IRE), downloaded from the RCSB Protein Data Bank.
Dengue virus — Structure of dengue virus — cryo-EM structure, 2002 (PDB 1K4R), downloaded from the RCSB Protein Data Bank.
AAV2 capsid — The atomic structure of adeno-associated virus (aav-2), a vector for human gene therapy — X-ray structure, 2002 (PDB 1LP3), downloaded from the RCSB Protein Data Bank.
AAV9 capsid — Structural characterization of adeno-associated virus serotype 9 — X-ray structure, 2012 (PDB 3UX1), downloaded from the RCSB Protein Data Bank.
AAV8 capsid — Structure of adeno-associated virus serotype 8 — X-ray structure, 2008 (PDB 2QA0), downloaded from the RCSB Protein Data Bank.
Hepatitis B virus capsid — Human hepatitis b viral capsid (hbcag) — X-ray structure, 1999 (PDB 1QGT), downloaded from the RCSB Protein Data Bank.
Poliovirus — Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus — X-ray structure, 1989 (PDB 2PLV), downloaded from the RCSB Protein Data Bank.
Human rhinovirus 14 — The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure — X-ray structure, 1988 (PDB 4RHV), downloaded from the RCSB Protein Data Bank.
Norovirus capsid — Crystal structure analysis of norwalk virus capsid — X-ray structure, 2001 (PDB 1IHM), downloaded from the RCSB Protein Data Bank.
Tobacco mosaic virus — Visualization of protein-nucleic acid interactions in a virus. refined structure of intact tobacco mosaic virus at 2.9 angstroms resoluti… — fiber diffraction structure, 1989 (PDB 2TMV), downloaded from the RCSB Protein Data Bank.
Satellite tobacco mosaic virus — Satellite tobacco mosaic virus/rna complex — X-ray structure, 1998 (PDB 1A34), downloaded from the RCSB Protein Data Bank.
Cowpea mosaic virus — Cowpea mosaic virus (cpmv) — X-ray structure, 2003 (PDB 1NY7), downloaded from the RCSB Protein Data Bank.
Bacteriophage MS2 capsid — The refined structure of bacteriophage ms2 at 2.8 angstroms resolution — X-ray structure, 1995 (PDB 2MS2), downloaded from the RCSB Protein Data Bank.
Bacteriophage Qβ capsid — Bacteriophage q beta capsid — X-ray structure, 1996 (PDB 1QBE), downloaded from the RCSB Protein Data Bank.
Adenovirus hexon — Refinement of adenovirus type 5 hexon with cns — X-ray structure, 2003 (PDB 1P30), downloaded from the RCSB Protein Data Bank.
Adenovirus fiber knob — Crystal structure of the receptor-binding domain of adenovirus type 5 fiber protein at 1.7 angstroms resolution — X-ray structure, 1995 (PDB 1KNB), downloaded from the RCSB Protein Data Bank.
T4 lysozyme — Structure of bacteriophage t4 lysozyme refined at 1.7 angstroms resolution — X-ray structure, 1986 (PDB 2LZM), downloaded from the RCSB Protein Data Bank.
Lambda repressor bound to DNA — Refined 1.8 angstrom crystal structure of the lambda repressor-operator complex — X-ray structure, 1991 (PDB 1LMB), downloaded from the RCSB Protein Data Bank.
SARS-CoV spike — Sars spike glycoprotein, trypsin-cleaved, stabilized variant, c3 symmetry — cryo-EM structure, 2018 (PDB 6CRZ), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike D614G — Structural impact on sars-cov-2 spike protein by d614g substitution — cryo-EM structure, 2021 (PDB 7KRQ), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike (prefusion, full length) — Distinct conformational states of sars-cov-2 spike protein — cryo-EM structure, 2020 (PDB 6XR8), downloaded from the RCSB Protein Data Bank.
MERS-CoV spike with antibody — Mers s ectodomain trimer in complex with variable domain of neutralizing antibody g4 — cryo-EM structure, 2017 (PDB 5W9I), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike (stabilised) — Structure of sars-cov-2 3q-2p full-length prefusion spike trimer (c3 symmetry) — cryo-EM structure, 2020 (PDB 7JJI), downloaded from the RCSB Protein Data Bank.
Human coronavirus spike — Prefusion structure of sars-cov spike glycoprotein, conformation 1 — cryo-EM structure, 2017 (PDB 5X58), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 RNA polymerase with remdesivir — The nsp12-nsp7-nsp8 complex bound to the template-primer rna and triphosphate form of remdesivir(rtp) — cryo-EM structure, 2020 (PDB 7BV2), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike with S309 antibody — Structure of the sars-cov-2 spike glycoprotein in complex with the s309 neutralizing antibody fab fragment — cryo-EM structure, 2020 (PDB 6WPS), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike with nanobody — Sars-cov-2 spike in complex with the s2m11 neutralizing antibody fab fragment — cryo-EM structure, 2020 (PDB 7K43), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 RBD with antibody CR3022 — Crystal structure of the sars-cov-2 receptor binding domain in complex with cr3022 fab — X-ray structure, 2020 (PDB 6YLA), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike–ACE2 complex — Sars-cov-2 s-ace2 complex — cryo-EM structure, 2020 (PDB 7DF4), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 RBD with CR3022 — Crystal structure of sars-cov-2 receptor binding domain in complex with human antibody cr3022 — X-ray structure, 2020 (PDB 6W41), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 RBD with ACE2 (chimera) — Structure of sars-cov-2 chimeric receptor-binding domain complexed with its receptor human ace2 — X-ray structure, 2020 (PDB 6VW1), downloaded from the RCSB Protein Data Bank.
ACE2–B0AT1 with spike RBD — The 2019-ncov rbd/ace2-b0at1 complex — cryo-EM structure, 2020 (PDB 6M17), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike with antibody 4A8 — S protein of sars-cov-2 in complex bound with 4a8 — cryo-EM structure, 2020 (PDB 7C2L), downloaded from the RCSB Protein Data Bank.
SARS-CoV-2 spike (closed, 2P) — Uncleavable spike protein of sars-cov-2 in closed conformation — cryo-EM structure, 2020 (PDB 6ZGE), downloaded from the RCSB Protein Data Bank.
HIV-1 capsid (mature lattice) — Atomic-level structure of the entire hiv-1 capsid (186 hexamers + 12 pentamers) — cryo-EM structure, 2013 (PDB 3J3Y), downloaded from the RCSB Protein Data Bank.
HIV-1 capsid hexamer — Structure of the native full-length hiv-1 capsid protein — X-ray structure, 2015 (PDB 4XFX), downloaded from the RCSB Protein Data Bank.
HIV-1 Env trimer with broadly neutralising antibodies — Hiv-1 bnab 1-18 in complex with bg505 sosip.664 and 10-1074 — cryo-EM structure, 2020 (PDB 6UDJ), downloaded from the RCSB Protein Data Bank.
Influenza HA stem with antibody — Crystal structure of the a/hong kong/1/1968 (h3n2) influenza virus hemagglutinin — X-ray structure, 2012 (PDB 4FNK), downloaded from the RCSB Protein Data Bank.
H1N1 hemagglutinin (2009) — Crystal structure of a 2009 h1n1 influenza virus hemagglutinin — X-ray structure, 2010 (PDB 3LZG), downloaded from the RCSB Protein Data Bank.
H7N9 hemagglutinin — Crystal structure of 2009 pandemic influenza virus hemagglutinin complexed with human receptor analogue lstc — X-ray structure, 2013 (PDB 4JTV), downloaded from the RCSB Protein Data Bank.
Influenza HA (H3) — Refinement of the influenza virus hemagglutinin by simulated annealing — X-ray structure, 1991 (PDB 5HMG), downloaded from the RCSB Protein Data Bank.
Influenza HA (H5) — Influenza virus hemagglutinin — X-ray structure, 1998 (PDB 2VIU), downloaded from the RCSB Protein Data Bank.
Neuraminidase with oseltamivir — Crystal structure of 2009 pandemic h1n1 neuraminidase complexed with oseltamivir — X-ray structure, 2011 (PDB 3TI6), downloaded from the RCSB Protein Data Bank.
Neuraminidase with oseltamivir (N1) — N1 neuraminidase in complex with oseltamivir 2 — X-ray structure, 2006 (PDB 2HU4), downloaded from the RCSB Protein Data Bank.
Swine H1 hemagglutinin with receptor analogue — 1930 swine h1 hemagglutinin complexed with lsta — X-ray structure, 2004 (PDB 1RV0), downloaded from the RCSB Protein Data Bank.
RSV F prefusion — Crystal structure of rsv f b9320 ds-cav1 — X-ray structure, 2017 (PDB 5UDE), downloaded from the RCSB Protein Data Bank.
RSV F (prefusion-stabilised vaccine design) — Crystal structure of prefusion-stabilized rsv f variant sc-tm — X-ray structure, 2015 (PDB 5C6B), downloaded from the RCSB Protein Data Bank.
SARS-CoV spike with neutralising antibody S230 — Sars-cov complex with human neutralizing s230 antibody fab fragment (state 1) — cryo-EM structure, 2019 (PDB 6NB6), downloaded from the RCSB Protein Data Bank.
Zika E protein — Cryo-em structure of zika virus complexed with fab c10 at ph 8.0 — cryo-EM structure, 2016 (PDB 5H37), downloaded from the RCSB Protein Data Bank.
Dengue E protein — Crystal structure of the dengue 2 virus envelope protein — X-ray structure, 2003 (PDB 1OAN), downloaded from the RCSB Protein Data Bank.
Dengue virus (mature) — Cryoem structure of dengue virus — cryo-EM structure, 2012 (PDB 3J27), downloaded from the RCSB Protein Data Bank.
Poliovirus with drug — Crystal structure of mahoney strain of poliovirus at 2.2a resolution — X-ray structure, 2002 (PDB 1HXS), downloaded from the RCSB Protein Data Bank.
Adenovirus penton dodecahedron — Dodecahedron formed of penton base protein from adenovirus ad3 — X-ray structure, 2012 (PDB 4AQQ), downloaded from the RCSB Protein Data Bank.
L-A virus capsid (yeast) — Structure of the l-a virus — X-ray structure, 2002 (PDB 1M1C), downloaded from the RCSB Protein Data Bank.
Equine rhinitis A virus — Equine rhinitis a virus — X-ray structure, 2010 (PDB 2WFF), downloaded from the RCSB Protein Data Bank.
Satellite tobacco necrosis virus — Satellite tobacco necrosis virus — X-ray structure, 2005 (PDB 2BUK), downloaded from the RCSB Protein Data Bank.
HPV16 L1 capsomere — L1 protein of human papillomavirus 16 — X-ray structure, 2000 (PDB 1DZL), downloaded from the RCSB Protein Data Bank.
HPV capsid — Bovine papillomavirus type 1 outer capsid — cryo-EM structure, 2010 (PDB 3IYJ), downloaded from the RCSB Protein Data Bank.
Herpes simplex virus 1 capsid — Cryoem structure of herpes simplex virus 1 capsid with associated tegument protein complexes. — cryo-EM structure, 2018 (PDB 6CGR), downloaded from the RCSB Protein Data Bank.
AAV2 bound to its receptor AAVR — Adeno-associated virus 2 in complex with aavr — cryo-EM structure, 2019 (PDB 6IHB), downloaded from the RCSB Protein Data Bank.
AAV2 capsid (VLP) — Structure of adeno-associated virus type 2 vlp — cryo-EM structure, 2016 (PDB 5IPI), downloaded from the RCSB Protein Data Bank.
Canine parvovirus empty capsid — Canine panleukopenia virus empty capsid structure — X-ray structure, 2000 (PDB 1C8D), downloaded from the RCSB Protein Data Bank.
Adenovirus capsid — Revised crystal structure of human adenovirus — X-ray structure, 2018 (PDB 6CGV), downloaded from the RCSB Protein Data Bank.
Ebola GP with antibody — Crystal structure of ebola glycoprotein — X-ray structure, 2016 (PDB 5JQ3), downloaded from the RCSB Protein Data Bank.
Brome mosaic virus — Novel inter-subunit contacts in barley stripe mosaic virus revealed by cryo-em — cryo-EM structure, 2015 (PDB 5A79), downloaded from the RCSB Protein Data Bank.
Black beetle virus — The refined three-dimensional structure of an insect virus at 2.8 angstroms resolution — X-ray structure, 1994 (PDB 2BBV), downloaded from the RCSB Protein Data Bank.
SV40 capsid — Simian virus 40 — X-ray structure, 1996 (PDB 1SVA), downloaded from the RCSB Protein Data Bank.
Pariacoto virus — The structure of pariacoto virus reveals a dodecahedral cage of duplex rna — X-ray structure, 2000 (PDB 1F8V), downloaded from the RCSB Protein Data Bank.
Echovirus 7 — Crystal structure echovirus 7 — X-ray structure, 2010 (PDB 2X5I), downloaded from the RCSB Protein Data Bank.
HIV integrase intasome — Crystal structure of the hiv-1 integrase core domain to 1.4a — X-ray structure, 2010 (PDB 3L3U), downloaded from the RCSB Protein Data Bank.
HIV RT with nevirapine — High resolution structures of hiv-1 rt from four rt-inhibitor complexes — X-ray structure, 1996 (PDB 1VRT), downloaded from the RCSB Protein Data Bank.
HIV protease with inhibitor — Crystal structure of a complex of hiv-1 protease with a dihydroethylene-containing inhibitor: comparisons with molecular modeling — X-ray structure, 1993 (PDB 1HIV), downloaded from the RCSB Protein Data Bank.
HIV protease with darunavir — Wild type hiv-1 protease with antiviral drug saquinavir — X-ray structure, 2010 (PDB 3OXC), downloaded from the RCSB Protein Data Bank.
HIV protease (mature) — Crystal structure of hiv1 protease in situ product complex — X-ray structure, 2006 (PDB 2NPH), downloaded from the RCSB Protein Data Bank.
Drug-resistant HIV protease with inhibitor — Crystal structure of the complex of mutant hiv-1 protease (l63p, a71v, v82t, i84v) with a hydroxyethylamine peptidomimetic inhibitor boc-… — X-ray structure, 2006 (PDB 1Z8C), downloaded from the RCSB Protein Data Bank.
RSV fusion protein core — Human respiratory syncytial virus fusion protein core — X-ray structure, 2001 (PDB 1G2C), downloaded from the RCSB Protein Data Bank.
MERS spike with antibody G4 — Mers s ectodomain trimer in complex with variable domain of neutralizing antibody g4 — cryo-EM structure, 2017 (PDB 5W9O), downloaded from the RCSB Protein Data Bank.