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8qv4

Hexameric HIV-1 CA in complex with DDD01728503

Method: X-RAY DIFFRACTION Dmax: 79.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spacer peptide 1

Human immunodeficiency virus 1

UniProt P12493

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 133–363 Not recorded EDO 1,2-ETHANEDIOL × 12 WZX ethyl 2-(3-oxidanylidene-2,4-dihydroquinoxalin-1-yl)ethanoate × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN Resolution 2.70 Å R-free 0.303

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8QV4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GWP STRUCTURE OF THE N-TERMINAL DOMAIN OF THE MATURE HIV-1 CAPSID PROTEIN Deposited 2002-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 132–282（151 aa） Fragment：AMINO-TERMINAL CORE DOMAIN RESIDUES 132 - 282
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 10；Pressure 1
Resolution not provided
1HIW TRIMERIC HIV-1 MATRIX PROTEIN Deposited 1996-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–131（131 aa） Fragment：CORE PROTEIN P17, RESIDUES 1 - 131 OF GAG POLYPROTEIN WITH N-TERMINAL HIS AND MET
Chain B 1–131（131 aa） Fragment：CORE PROTEIN P17, RESIDUES 1 - 131 OF GAG POLYPROTEIN WITH N-TERMINAL HIS AND MET
Chain C 1–131（131 aa） Fragment：CORE PROTEIN P17, RESIDUES 1 - 131 OF GAG POLYPROTEIN WITH N-TERMINAL HIS AND MET
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.332
1HIW TRIMERIC HIV-1 MATRIX PROTEIN Deposited 1996-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain Q 1–131（131 aa） Fragment：CORE PROTEIN P17, RESIDUES 1 - 131 OF GAG POLYPROTEIN WITH N-TERMINAL HIS AND MET
Chain R 1–131（131 aa） Fragment：CORE PROTEIN P17, RESIDUES 1 - 131 OF GAG POLYPROTEIN WITH N-TERMINAL HIS AND MET
Chain S 1–131（131 aa） Fragment：CORE PROTEIN P17, RESIDUES 1 - 131 OF GAG POLYPROTEIN WITH N-TERMINAL HIS AND MET
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.332
1UPH HIV-1 Myristoylated Matrix Deposited 2003-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–131（131 aa） Fragment：RESIDUES 1-131
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；308 K；Ionic strength (raw mmCIF value) 100MM NACL；Pressure 1
Resolution not provided
2C55 Solution Structure of the Human Immunodeficiency Virus Type 1 p6 Protein Deposited 2005-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 448–499（52 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3；300 K；Pressure 1.0
NMR sample composition 50% WATER/50% TFE-D2
Resolution not provided
2X2D acetyl-CypA:HIV-1 N-term capsid domain complex Deposited 2010-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 133–278（146 aa） Fragment：RESIDUES 133-278
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å R-free 0.257
2X2D acetyl-CypA:HIV-1 N-term capsid domain complex Deposited 2010-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 133–278（146 aa） Fragment：RESIDUES 133-278
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å R-free 0.257
3GV2 X-ray Structure of Hexameric HIV-1 CA Deposited 2009-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–351（219 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK
Chain B 133–351（219 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK
Chain C 133–351（219 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK
Chain D 133–351（219 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK
Chain E 133–351（219 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK
Chain F 133–351（219 aa） Fragment：UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK
Mutation：W184A,M185A Mutation：W184A,M185A Mutation：W184A,M185A Mutation：W184A,M185A Mutation：W184A,M185A Mutation：W184A,M185A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M imidazole, pH 6.5, 600 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 7.00 Å R-free 0.323
4U0A Hexameric HIV-1 CA in complex with CPSF6 peptide, P6 crystal form Deposited 2014-07-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: Dodecameric
Chain A 133–363（231 aa）
Mutation：A14C,E45C,W184A,M185A CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.6M sodium potassium tartrate tetrahydrate, 0.1M TRIS
Resolution 2.05 Å R-free 0.253
4U0B Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form Deposited 2014-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: Dodecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Mutation：yes Mutation：yes Mutation：yes Mutation：yes Mutation：yes Mutation：yes No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；20% v/v PEG 300, 10% v/v glycerol, 5% w/v PEG 8K, 0.1 M TRIS
Resolution 2.80 Å R-free 0.262
4U0B Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form Deposited 2014-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: Dodecameric
Chain G 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain J 133–363（231 aa）
Chain K 133–363（231 aa）
Chain L 133–363（231 aa）
Mutation：yes Mutation：yes Mutation：yes Mutation：yes Mutation：yes Mutation：yes No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；20% v/v PEG 300, 10% v/v glycerol, 5% w/v PEG 8K, 0.1 M TRIS
Resolution 2.80 Å R-free 0.262
4U0C Hexameric HIV-1 CA in complex with Nup153 peptide, P6 crystal form Deposited 2014-07-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: Dodecameric
Chain A 133–363（231 aa）
Mutation：yes No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；290 K；30% v/v PEG 400, 0.1 M CHES
Resolution 1.77 Å R-free 0.211
4U0D Hexameric HIV-1 CA in complex with Nup153 peptide, P212121 crystal form Deposited 2014-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: Nonameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Mutation：yes Mutation：yes Mutation：yes Mutation：yes Mutation：yes Mutation：yes CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；10% w/v PEG 8K, 0.1M imidazole
Resolution 3.00 Å R-free 0.267
4U0D Hexameric HIV-1 CA in complex with Nup153 peptide, P212121 crystal form Deposited 2014-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: Nonameric
Chain G 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain J 133–363（231 aa）
Chain K 133–363（231 aa）
Chain L 133–363（231 aa）
Mutation：yes Mutation：yes Mutation：yes Mutation：yes Mutation：yes Mutation：yes No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；10% w/v PEG 8K, 0.1M imidazole
Resolution 3.00 Å R-free 0.267
4U0E Hexameric HIV-1 CA in complex with PF3450074 Deposited 2014-07-11 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: Hexameric
Chain A 133–363（231 aa）
Mutation：yes CL CHLORIDE ION × 6 1B0 N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.2 M magnesium chloride, 8% w/v PEG 20K, 8% v/v PEG 550 MME, 0.1 M TRIS pH 8.5, 3% w/v 1,5-diaminopentane dihydrochloride
Resolution 2.04 Å R-free 0.239
4U0F Hexameric HIV-1 CA in Complex with BI-2 Deposited 2014-07-11 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: Hexameric
Chain A 133–363（231 aa）
Mutation：yes EDO 1,2-ETHANEDIOL × 6 3A8 (4S)-4-(4-hydroxyphenyl)-3-phenyl-4,5-dihydropyrrolo[3,4-c]pyrazol-6(1H)-one × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；12% w/v PEG 4K, 0.1 M TRIS pH 8.5, 3% v/v ethylene glycol
Resolution 2.22 Å R-free 0.270
4XFX Structure of the native full-length HIV-1 capsid protein Deposited 2014-12-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded IOD IODIDE ION × 42 CL CHLORIDE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, MMT
Resolution 2.43 Å R-free 0.249
4XFY Structure of the native full-length dehydrated HIV-1 capsid protein Deposited 2014-12-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded CL CHLORIDE ION × 12 1PE PENTAETHYLENE GLYCOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG3350, NaI, Sodium cacodylate
Resolution 2.80 Å R-free 0.250
4XFZ Structure of the native full-length HIV-1 capsid protein in complex with PF-3450074 (PF74) Deposited 2014-12-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded IOD IODIDE ION × 36 CL CHLORIDE ION × 12 1B0 N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate
Resolution 2.70 Å R-free 0.241
4XRO Disulfide stabilized HIV-1 CA hexamer 4mut (S41A, Q67H, V165I, L172I) Deposited 2015-01-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：A14C,S41A,E45C,Q67H,V165I,L172I,W184A,M185A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1 M NaCl, 12% w/v PEG 4K, 0.1 M TRIS pH 8.5, 4% v/v formamide
Resolution 2.01 Å R-free 0.226
4XRQ Disulfide stabilized HIV-1 CA hexamer 4mut (S41A, Q67H, V165I, L172I) in complex with PF-3450074 Deposited 2015-01-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：A14C,S41A,E45C,Q67H,V165I,L172I,W184A,M185A 1B0 N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.2 M potassium thiocyanate, 8% w/v PEG 20K, 8% v/v PEG 550 MME, 0.1 M TRIS pH 8.5, 3% 1,4-dioxane
Resolution 1.95 Å R-free 0.221
5HGL Hexameric HIV-1 CA, open conformation Deposited 2016-01-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Mutation：C14A, C45E, A184W, A185M Mutation：C14A, C45E, A184W, A185M Mutation：C14A, C45E, A184W, A185M Mutation：C14A, C45E, A184W, A185M Mutation：C14A, C45E, A184W, A185M Mutation：C14A, C45E, A184W, A185M 1B0 N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5)
Resolution 3.10 Å R-free 0.282
5HGM Hexameric HIV-1 CA in complex with dATP Deposited 2016-01-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：C14A, C45E, A184W, A185M DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5), 10mM dATP
Resolution 2.04 Å R-free 0.263
5HGN Hexameric HIV-1 CA, apo form Deposited 2016-01-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：C14A, C45E, A184W, A185M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5)
Resolution 1.90 Å R-free 0.223
5HGO Hexameric HIV-1 CA R18G mutant Deposited 2016-01-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：C14A, C45E, A184W, A185M, R18G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5)
Resolution 2.00 Å R-free 0.221
5HGP Hexameric HIV-1 CA in complex with hexacarboxybenzene Deposited 2016-01-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：C14A, C45E, A184W, A185M BHC BENZENE HEXACARBOXYLIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5), Mellitic acid (1mM). Mellitic acid stock was adjusted to pH 8.0 with TRIS prior to setting up trays.
Resolution 1.95 Å R-free 0.221
5IRT Dimerization interface of the noncrystalline HIV-1 capsid protein lattice from solid state NMR spectroscopy of tubular assemblies Deposited 2016-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 8；278 K；Ionic strength (raw mmCIF value) 1；Pressure 1
NMR sample composition 15 mM U-15N,13C-Met and U-15N Capsid protein, water | water
NMR sample composition 15 mM 2-13C-glycerol and U-15N Capsid protein, water | water
NMR sample composition 15 mM 2-13C-glycerol, U-15N, unlabeled Tyr and Phe Capsid protein, water | water
NMR sample composition 7.5 mM Methyl-13C-Met Capsid protein-1, 7.5 mM 15N-indole Capsid protein-2, water | water
NMR sample composition 15 mM Methyl-13C-Met, 2-13C-indole, U-15N Capsid protein, water | water
Resolution not provided
5JPA Hexameric HIV-1 CA H12Y mutant Deposited 2016-05-03 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：H12Y, A14C, E45C, W184A, M185A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；PEG 550MME (12% w/v), KSCN (0.15M), 0.1M TRIS
Resolution 1.70 Å R-free 0.232
5L93 An atomic model of HIV-1 CA-SP1 reveals structures regulating assembly and maturation Deposited 2016-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 148–371（224 aa）
Chain B 148–371（224 aa）
Chain C 148–371（224 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；Virus-like particles were assembled in the presence of nucleic acid (73mer oligonucleotide, 1:10 molar ratio oligonucleotide:protein).
cryo-EM vitrification conditions Cryogen ETHANE；10nM colloidal gold was added to the sample prior to plunge freezing.
Resolution 3.90 Å
5O2U Llama VHH in complex with p24 Deposited 2017-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–500（500 aa）
Chain C 1–500（500 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Tris base pH 8.0, Polyethylene glycol (PEG) 6000 25% Ethylene Glycol
Resolution 2.76 Å R-free 0.256
5TSV HIV-1 CA hexamer with NUP153 peptide - R3 crystal form Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Not recorded FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris, pH 8.2 12% PEG 8000 2% Tacsimate
Resolution 2.50 Å R-free 0.251
5TSX HIV-1 CA hexamer with NUP153 peptide - P1 crystal form Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain K 133–363（231 aa）
Not recorded FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris, pH 9 12% PEG 8000
Resolution 1.90 Å R-free 0.228
5TSX HIV-1 CA hexamer with NUP153 peptide - P1 crystal form Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain F 133–363（231 aa）
Chain G 133–363（231 aa）
Chain J 133–363（231 aa）
Chain L 133–363（231 aa）
Not recorded FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris, pH 9 12% PEG 8000
Resolution 1.90 Å R-free 0.228
5UPW CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations Deposited 2017-02-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–353（221 aa） Fragment：UNP residues 133-353
Chain B 133–353（221 aa） Fragment：UNP residues 133-353
Chain C 133–353（221 aa） Fragment：UNP residues 133-353
Chain D 133–353（221 aa） Fragment：UNP residues 133-353
Chain E 133–353（221 aa） Fragment：UNP residues 133-353
Chain F 133–353（221 aa） Fragment：UNP residues 133-353
Mutation：A92E Mutation：A92E Mutation：A92E Mutation：A92E Mutation：A92E Mutation：A92E No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；The assembled sample (1.5 microliter) was applied to the carbon side of a glow discharged perforated Quantifoil grid, followed by application of 3 microliter of low salt buffer (100 milimolar NaCl, 50 milimolar Tris pH 8.0) on the back side of the grid, and blotting, from the back side, with a filter paper, before plunge-freezing in liquid ethane
Resolution 5.00 Å
6AYA Structure of the native full-length HIV-1 capsid protein in complex with Nup153 peptide Deposited 2017-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 133–363（231 aa）
Not recorded IOD IODIDE ION × 42 CL CHLORIDE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, MIB, Glycerol
Resolution 2.40 Å R-free 0.274
6BHS HIV-1 CA hexamer in complex with IP6, hexagonal crystal form Deposited 2017-10-31 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：A146C, E177C, W316A, M317A IHP INOSITOL HEXAKISPHOSPHATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；10% PEG 8,000, 2% Tacsimate, 0.1 M Tris
Resolution 1.98 Å R-free 0.284
6BHT HIV-1 CA hexamer in complex with IP6, orthorhombic crystal form Deposited 2017-10-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A IHP INOSITOL HEXAKISPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290 K；8% PEG 8000, 0.1M Tris
Resolution 2.69 Å R-free 0.255
6BHT HIV-1 CA hexamer in complex with IP6, orthorhombic crystal form Deposited 2017-10-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain G 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain J 133–363（231 aa）
Chain K 133–363（231 aa）
Chain L 133–363（231 aa）
Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A Mutation：A146C, E177C, W316A, M317A IHP INOSITOL HEXAKISPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；290 K；8% PEG 8000, 0.1M Tris
Resolution 2.69 Å R-free 0.255
6H09 HIV capsid hexamer with IP6 ligand Deposited 2018-07-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–351（219 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；293 K；PEG 4K
Resolution 2.00 Å R-free 0.266
6WAP Atomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle Spinning NMR Deposited 2020-03-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–363（231 aa）
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 6；277 K；Ionic strength (raw mmCIF value) 2.4；Pressure 1
NMR sample composition 100 % [U-13C; U-15N] HIV-1 capsid protein, solid | solid
NMR sample composition 100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein, solid | solid
NMR sample composition 100 % [2-13C]-Glucose,U-15N HIV-1 capsid protein, solid | solid
NMR sample composition 100 % 13C,15N-His HIV-1 capsid protein, solid | solid
NMR sample composition 100 % 13C,15N-Tyr HIV-1 capsid protein, solid | solid
NMR sample composition 50 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Ile HIV-1 capsid protein, solid | solid
NMR sample composition 50 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Val HIV-1 capsid protein, solid | solid
NMR sample composition 86 % HIV-1 capsid protein, 14 % U-13C,15N-CA HIV-1 capsid protein, solid | solid
NMR sample composition 50 % [U-13C] HIV-1 capsid protein, 50 % [U-15N] HIV-1 capsid protein, solid | solid
Resolution not provided
6X63 Atomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle Spinning NMR Deposited 2020-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 378 PDB declaration: 378-meric
Chain 0 133–363（231 aa）
Chain 0A 133–363（231 aa）
Chain 0B 133–363（231 aa）
Chain 0C 133–363（231 aa）
Chain 0D 133–363（231 aa）
Chain 0E 133–363（231 aa）
Chain 1 133–363（231 aa）
Chain 1A 133–363（231 aa）
Chain 1B 133–363（231 aa）
Chain 1C 133–363（231 aa）
Chain 1D 133–363（231 aa）
Chain 1E 133–363（231 aa）
Chain 2 133–363（231 aa）
Chain 2A 133–363（231 aa）
Chain 2B 133–363（231 aa）
Chain 2C 133–363（231 aa）
Chain 2D 133–363（231 aa）
Chain 2E 133–363（231 aa）
Chain 3 133–363（231 aa）
Chain 3A 133–363（231 aa）
Chain 3B 133–363（231 aa）
Chain 3C 133–363（231 aa）
Chain 3D 133–363（231 aa）
Chain 3E 133–363（231 aa）
Chain 4 133–363（231 aa）
Chain 4A 133–363（231 aa）
Chain 4B 133–363（231 aa）
Chain 4C 133–363（231 aa）
Chain 4D 133–363（231 aa）
Chain 4E 133–363（231 aa）
Chain 5 133–363（231 aa）
Chain 5A 133–363（231 aa）
Chain 5B 133–363（231 aa）
Chain 5C 133–363（231 aa）
Chain 5D 133–363（231 aa）
Chain 5E 133–363（231 aa）
Chain 6 133–363（231 aa）
Chain 6A 133–363（231 aa）
Chain 6B 133–363（231 aa）
Chain 6C 133–363（231 aa）
Chain 6D 133–363（231 aa）
Chain 6E 133–363（231 aa）
Chain 7 133–363（231 aa）
Chain 7A 133–363（231 aa）
Chain 7B 133–363（231 aa）
Chain 7C 133–363（231 aa）
Chain 7D 133–363（231 aa）
Chain 7E 133–363（231 aa）
Chain 8 133–363（231 aa）
Chain 8A 133–363（231 aa）
Chain 8B 133–363（231 aa）
Chain 8C 133–363（231 aa）
Chain 8D 133–363（231 aa）
Chain 8E 133–363（231 aa）
Chain 9 133–363（231 aa）
Chain 9A 133–363（231 aa）
Chain 9B 133–363（231 aa）
Chain 9C 133–363（231 aa）
Chain 9D 133–363（231 aa）
Chain 9E 133–363（231 aa）
Chain A 133–363（231 aa）
Chain AA 133–363（231 aa）
Chain AB 133–363（231 aa）
Chain AC 133–363（231 aa）
Chain AD 133–363（231 aa）
Chain AE 133–363（231 aa）
Chain AF 133–363（231 aa）
Chain B 133–363（231 aa）
Chain BA 133–363（231 aa）
Chain BB 133–363（231 aa）
Chain BC 133–363（231 aa）
Chain BD 133–363（231 aa）
Chain BE 133–363（231 aa）
Chain BF 133–363（231 aa）
Chain C 133–363（231 aa）
Chain CA 133–363（231 aa）
Chain CB 133–363（231 aa）
Chain CC 133–363（231 aa）
Chain CD 133–363（231 aa）
Chain CE 133–363（231 aa）
Chain CF 133–363（231 aa）
Chain D 133–363（231 aa）
Chain DA 133–363（231 aa）
Chain DB 133–363（231 aa）
Chain DC 133–363（231 aa）
Chain DD 133–363（231 aa）
Chain DE 133–363（231 aa）
Chain DF 133–363（231 aa）
Chain E 133–363（231 aa）
Chain EA 133–363（231 aa）
Chain EB 133–363（231 aa）
Chain EC 133–363（231 aa）
Chain ED 133–363（231 aa）
Chain EE 133–363（231 aa）
Chain EF 133–363（231 aa）
Chain F 133–363（231 aa）
Chain FA 133–363（231 aa）
Chain FB 133–363（231 aa）
Chain FC 133–363（231 aa）
Chain FD 133–363（231 aa）
Chain FE 133–363（231 aa）
Chain FF 133–363（231 aa）
Chain G 133–363（231 aa）
Chain GA 133–363（231 aa）
Chain GB 133–363（231 aa）
Chain GC 133–363（231 aa）
Chain GD 133–363（231 aa）
Chain GE 133–363（231 aa）
Chain H 133–363（231 aa）
Chain HA 133–363（231 aa）
Chain HB 133–363（231 aa）
Chain HC 133–363（231 aa）
Chain HD 133–363（231 aa）
Chain HE 133–363（231 aa）
Chain I 133–363（231 aa）
Chain IA 133–363（231 aa）
Chain IB 133–363（231 aa）
Chain IC 133–363（231 aa）
Chain ID 133–363（231 aa）
Chain IE 133–363（231 aa）
Chain J 133–363（231 aa）
Chain JA 133–363（231 aa）
Chain JB 133–363（231 aa）
Chain JC 133–363（231 aa）
Chain JD 133–363（231 aa）
Chain JE 133–363（231 aa）
Chain K 133–363（231 aa）
Chain KA 133–363（231 aa）
Chain KB 133–363（231 aa）
Chain KC 133–363（231 aa）
Chain KD 133–363（231 aa）
Chain KE 133–363（231 aa）
Chain L 133–363（231 aa）
Chain LA 133–363（231 aa）
Chain LB 133–363（231 aa）
Chain LC 133–363（231 aa）
Chain LD 133–363（231 aa）
Chain LE 133–363（231 aa）
Chain M 133–363（231 aa）
Chain MA 133–363（231 aa）
Chain MB 133–363（231 aa）
Chain MC 133–363（231 aa）
Chain MD 133–363（231 aa）
Chain ME 133–363（231 aa）
Chain N 133–363（231 aa）
Chain NA 133–363（231 aa）
Chain NB 133–363（231 aa）
Chain NC 133–363（231 aa）
Chain ND 133–363（231 aa）
Chain NE 133–363（231 aa）
Chain O 133–363（231 aa）
Chain OA 133–363（231 aa）
Chain OB 133–363（231 aa）
Chain OC 133–363（231 aa）
Chain OD 133–363（231 aa）
Chain OE 133–363（231 aa）
Chain P 133–363（231 aa）
Chain PA 133–363（231 aa）
Chain PB 133–363（231 aa）
Chain PC 133–363（231 aa）
Chain PD 133–363（231 aa）
Chain PE 133–363（231 aa）
Chain Q 133–363（231 aa）
Chain QA 133–363（231 aa）
Chain QB 133–363（231 aa）
Chain QC 133–363（231 aa）
Chain QD 133–363（231 aa）
Chain QE 133–363（231 aa）
Chain R 133–363（231 aa）
Chain RA 133–363（231 aa）
Chain RB 133–363（231 aa）
Chain RC 133–363（231 aa）
Chain RD 133–363（231 aa）
Chain RE 133–363（231 aa）
Chain S 133–363（231 aa）
Chain SA 133–363（231 aa）
Chain SB 133–363（231 aa）
Chain SC 133–363（231 aa）
Chain SD 133–363（231 aa）
Chain SE 133–363（231 aa）
Chain T 133–363（231 aa）
Chain TA 133–363（231 aa）
Chain TB 133–363（231 aa）
Chain TC 133–363（231 aa）
Chain TD 133–363（231 aa）
Chain TE 133–363（231 aa）
Chain U 133–363（231 aa）
Chain UA 133–363（231 aa）
Chain UB 133–363（231 aa）
Chain UC 133–363（231 aa）
Chain UD 133–363（231 aa）
Chain UE 133–363（231 aa）
Chain V 133–363（231 aa）
Chain VA 133–363（231 aa）
Chain VB 133–363（231 aa）
Chain VC 133–363（231 aa）
Chain VD 133–363（231 aa）
Chain VE 133–363（231 aa）
Chain W 133–363（231 aa）
Chain WA 133–363（231 aa）
Chain WB 133–363（231 aa）
Chain WC 133–363（231 aa）
Chain WD 133–363（231 aa）
Chain WE 133–363（231 aa）
Chain X 133–363（231 aa）
Chain XA 133–363（231 aa）
Chain XB 133–363（231 aa）
Chain XC 133–363（231 aa）
Chain XD 133–363（231 aa）
Chain XE 133–363（231 aa）
Chain Y 133–363（231 aa）
Chain YA 133–363（231 aa）
Chain YB 133–363（231 aa）
Chain YC 133–363（231 aa）
Chain YD 133–363（231 aa）
Chain YE 133–363（231 aa）
Chain Z 133–363（231 aa）
Chain ZA 133–363（231 aa）
Chain ZB 133–363（231 aa）
Chain ZC 133–363（231 aa）
Chain ZD 133–363（231 aa）
Chain ZE 133–363（231 aa）
Chain a 133–363（231 aa）
Chain aA 133–363（231 aa）
Chain aB 133–363（231 aa）
Chain aC 133–363（231 aa）
Chain aD 133–363（231 aa）
Chain aE 133–363（231 aa）
Chain b 133–363（231 aa）
Chain bA 133–363（231 aa）
Chain bB 133–363（231 aa）
Chain bC 133–363（231 aa）
Chain bD 133–363（231 aa）
Chain bE 133–363（231 aa）
Chain c 133–363（231 aa）
Chain cA 133–363（231 aa）
Chain cB 133–363（231 aa）
Chain cC 133–363（231 aa）
Chain cD 133–363（231 aa）
Chain cE 133–363（231 aa）
Chain d 133–363（231 aa）
Chain dA 133–363（231 aa）
Chain dB 133–363（231 aa）
Chain dC 133–363（231 aa）
Chain dD 133–363（231 aa）
Chain dE 133–363（231 aa）
Chain e 133–363（231 aa）
Chain eA 133–363（231 aa）
Chain eB 133–363（231 aa）
Chain eC 133–363（231 aa）
Chain eD 133–363（231 aa）
Chain eE 133–363（231 aa）
Chain f 133–363（231 aa）
Chain fA 133–363（231 aa）
Chain fB 133–363（231 aa）
Chain fC 133–363（231 aa）
Chain fD 133–363（231 aa）
Chain fE 133–363（231 aa）
Chain g 133–363（231 aa）
Chain gA 133–363（231 aa）
Chain gB 133–363（231 aa）
Chain gC 133–363（231 aa）
Chain gD 133–363（231 aa）
Chain gE 133–363（231 aa）
Chain h 133–363（231 aa）
Chain hA 133–363（231 aa）
Chain hB 133–363（231 aa）
Chain hC 133–363（231 aa）
Chain hD 133–363（231 aa）
Chain hE 133–363（231 aa）
Chain i 133–363（231 aa）
Chain iA 133–363（231 aa）
Chain iB 133–363（231 aa）
Chain iC 133–363（231 aa）
Chain iD 133–363（231 aa）
Chain iE 133–363（231 aa）
Chain j 133–363（231 aa）
Chain jA 133–363（231 aa）
Chain jB 133–363（231 aa）
Chain jC 133–363（231 aa）
Chain jD 133–363（231 aa）
Chain jE 133–363（231 aa）
Chain k 133–363（231 aa）
Chain kA 133–363（231 aa）
Chain kB 133–363（231 aa）
Chain kC 133–363（231 aa）
Chain kD 133–363（231 aa）
Chain kE 133–363（231 aa）
Chain l 133–363（231 aa）
Chain lA 133–363（231 aa）
Chain lB 133–363（231 aa）
Chain lC 133–363（231 aa）
Chain lD 133–363（231 aa）
Chain lE 133–363（231 aa）
Chain m 133–363（231 aa）
Chain mA 133–363（231 aa）
Chain mB 133–363（231 aa）
Chain mC 133–363（231 aa）
Chain mD 133–363（231 aa）
Chain mE 133–363（231 aa）
Chain n 133–363（231 aa）
Chain nA 133–363（231 aa）
Chain nB 133–363（231 aa）
Chain nC 133–363（231 aa）
Chain nD 133–363（231 aa）
Chain nE 133–363（231 aa）
Chain o 133–363（231 aa）
Chain oA 133–363（231 aa）
Chain oB 133–363（231 aa）
Chain oC 133–363（231 aa）
Chain oD 133–363（231 aa）
Chain oE 133–363（231 aa）
Chain p 133–363（231 aa）
Chain pA 133–363（231 aa）
Chain pB 133–363（231 aa）
Chain pC 133–363（231 aa）
Chain pD 133–363（231 aa）
Chain pE 133–363（231 aa）
Chain q 133–363（231 aa）
Chain qA 133–363（231 aa）
Chain qB 133–363（231 aa）
Chain qC 133–363（231 aa）
Chain qD 133–363（231 aa）
Chain qE 133–363（231 aa）
Chain r 133–363（231 aa）
Chain rA 133–363（231 aa）
Chain rB 133–363（231 aa）
Chain rC 133–363（231 aa）
Chain rD 133–363（231 aa）
Chain rE 133–363（231 aa）
Chain s 133–363（231 aa）
Chain sA 133–363（231 aa）
Chain sB 133–363（231 aa）
Chain sC 133–363（231 aa）
Chain sD 133–363（231 aa）
Chain sE 133–363（231 aa）
Chain t 133–363（231 aa）
Chain tA 133–363（231 aa）
Chain tB 133–363（231 aa）
Chain tC 133–363（231 aa）
Chain tD 133–363（231 aa）
Chain tE 133–363（231 aa）
Chain u 133–363（231 aa）
Chain uA 133–363（231 aa）
Chain uB 133–363（231 aa）
Chain uC 133–363（231 aa）
Chain uD 133–363（231 aa）
Chain uE 133–363（231 aa）
Chain v 133–363（231 aa）
Chain vA 133–363（231 aa）
Chain vB 133–363（231 aa）
Chain vC 133–363（231 aa）
Chain vD 133–363（231 aa）
Chain vE 133–363（231 aa）
Chain w 133–363（231 aa）
Chain wA 133–363（231 aa）
Chain wB 133–363（231 aa）
Chain wC 133–363（231 aa）
Chain wD 133–363（231 aa）
Chain wE 133–363（231 aa）
Chain x 133–363（231 aa）
Chain xA 133–363（231 aa）
Chain xB 133–363（231 aa）
Chain xC 133–363（231 aa）
Chain xD 133–363（231 aa）
Chain xE 133–363（231 aa）
Chain y 133–363（231 aa）
Chain yA 133–363（231 aa）
Chain yB 133–363（231 aa）
Chain yC 133–363（231 aa）
Chain yD 133–363（231 aa）
Chain yE 133–363（231 aa）
Chain z 133–363（231 aa）
Chain zA 133–363（231 aa）
Chain zB 133–363（231 aa）
Chain zC 133–363（231 aa）
Chain zD 133–363（231 aa）
Chain zE 133–363（231 aa）
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 6；277 K；Ionic strength (raw mmCIF value) 2.4；Pressure 1
NMR sample composition 100 % [U-13C; U-15N] HIV-1 capsid protein, solid | solid
NMR sample composition 100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein, solid | solid
NMR sample composition 100 % [2-13C]-Glucose,U-15N HIV-1 capsid protein, solid | solid
NMR sample composition 100 % 13C,15N-His HIV-1 capsid protein, solid | solid
NMR sample composition 100 % 13C,15N-Tyr HIV-1 capsid protein, solid | solid
NMR sample composition 50 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Ile HIV-1 capsid, solid | solid
NMR sample composition 50 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Val HIV-1 capsid, solid | solid
NMR sample composition 86 % HIV-1 capsid protein, 14 % U-13C,15N-CA HIV-1 capsid, solid | solid
NMR sample composition 50 % [U-13C] HIV-1 capsid protein, 50 % [U-15N] HIV-1 capsid, solid | solid
Resolution not provided
7M9F Structure of the wild-type native full-length HIV-1 capsid protein in complex with ZW-1261 Deposited 2021-03-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded YTG N-(4-chlorophenyl)-Nalpha-[(5-hydroxy-1H-indol-3-yl)acetyl]-N-methyl-L-phenylalaninamide × 6 IOD IODIDE ION × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, NaI, Sodium Cacodylate, Glycerol
Resolution 2.70 Å R-free 0.253
7QDF Hexameric HIV-1 (M-group) CA R120 mutant Deposited 2021-11-26 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain AAA 133–363（231 aa）
Mutation：R120 IOD IODIDE ION × 12 CL CHLORIDE ION × 30 BME BETA-MERCAPTOETHANOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；9.5% PEG 3350 (v/v), 310 mM NaI, 100 mM Sodium Cacodylate. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.
Resolution 2.30 Å R-free 0.278
7RAO Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer Deposited 2021-07-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Mutation：A14C, E45C, M66I, W184A, M185A Mutation：A14C, E45C, M66I, W184A, M185A IOD IODIDE ION × 18 CL CHLORIDE ION × 21 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.125-0.35M Sodium Iodide, 2-8% Peg 3350, 6% glycerol, 0.1M sodium cacodylate pH 6.5
Resolution 2.29 Å R-free 0.244
7RAO Structure of M66I mutant of disulfide stabilized HIV-1 CA hexamer Deposited 2021-07-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain C 133–363（231 aa）
Mutation：A14C, E45C, M66I, W184A, M185A IOD IODIDE ION × 24 CL CHLORIDE ION × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.125-0.35M Sodium Iodide, 2-8% Peg 3350, 6% glycerol, 0.1M sodium cacodylate pH 6.5
Resolution 2.29 Å R-free 0.244
7RAR Structure of Q67H mutant of disulfide stabilized HIV-1 CA hexamer Deposited 2021-07-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain C 133–363（231 aa）
Mutation：A14C, E45C, Q67H, W184A, M185A IOD IODIDE ION × 36 CL CHLORIDE ION × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.425M NaI, 4% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5
Resolution 2.15 Å R-free 0.240
7RHN Co-crystal structure of Q67H mutant of disulfide stabilized HIV-1 CA hexamer and lenacapavir Deposited 2021-07-17 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain C 133–363（231 aa）
Mutation：A14C, E45C, Q67H, W184A, M185A QNG Lenacapavir × 6 IOD IODIDE ION × 18 CL CHLORIDE ION × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.35M NaI, 4% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5
Resolution 2.46 Å R-free 0.288
7URN Structure of HIV-1 capsid declination Deposited 2022-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 35 PDB declaration: 35-meric
Chain A 133–363（231 aa）
Chain L 133–363（231 aa）
Chain M 133–363（231 aa）
Chain N 133–363（231 aa）
Chain O 133–363（231 aa）
Chain P 133–363（231 aa）
Chain Q 133–363（231 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 3.43 Å
8EJL Structure of HIV-1 capsid declination in complex with CPSF6-FG peptide Deposited 2022-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 133–363（231 aa）
Chain L 133–363（231 aa）
Chain M 133–363（231 aa）
Chain N 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 3.90 Å
8EJL Structure of HIV-1 capsid declination in complex with CPSF6-FG peptide Deposited 2022-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Chain L 133–363（231 aa）
Chain M 133–363（231 aa）
Chain N 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 3.90 Å
8EJL Structure of HIV-1 capsid declination in complex with CPSF6-FG peptide Deposited 2022-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Chain L 133–363（231 aa）
Chain M 133–363（231 aa）
Chain N 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 3.90 Å
8QUB Hexameric HIV-1 CA in complex with DDD00074110 Deposited 2023-10-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded WVZ (1~{S})-1-phenyl-2,4-dihydro-1~{H}-isoquinolin-3-one × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 1.63 Å R-free 0.210
8QUH Hexameric HIV-1 CA in complex with DDD00057456 Deposited 2023-10-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded AJ2 4-methylquinolin-2-ol × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 1.55 Å R-free 0.195
8QUI Hexameric HIV-1 CA in complex with DDD00024969 Deposited 2023-10-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded XXL ethyl (3-oxo-2,3-dihydro-4H-1,4-benzoxazin-4-yl)acetate × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 1.69 Å R-free 0.216
8QUJ Hexameric HIV-1 CA in complex with DDD00100452 Deposited 2023-10-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded EDO 1,2-ETHANEDIOL × 24 WWR 3-(phenylmethyl)-1~{H}-imidazol-2-one × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 1.63 Å R-free 0.200
8QUK Hexameric HIV-1 CA in complex with DDD00100439 Deposited 2023-10-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded EDO 1,2-ETHANEDIOL × 12 WVU (phenylmethyl) 3-oxidanylidenepiperazine-1-carboxylate × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 1.38 Å R-free 0.203
8QUL Hexameric HIV-1 CA in complex with DDD00100555 Deposited 2023-10-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded 3IP 3-(BENZYLOXY)PYRIDIN-2-AMINE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 1.67 Å R-free 0.210
8QUW Hexameric HIV-1 CA in complex with DDD01044153 Deposited 2023-10-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded WZR (4~{R})-7-oxidanyl-4-phenyl-3,4-dihydro-1~{H}-quinolin-2-one × 6 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 2.02 Å R-free 0.230
8QUX Hexameric HIV-1 CA in complex with DDD00100333 Deposited 2023-10-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded EDO 1,2-ETHANEDIOL × 12 S0I 4-benzyl-3,4-dihydroquinoxalin-2(1H)-one × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 2.30 Å R-free 0.276
8QUY Hexameric HIV-1 CA in complex with DDD01728501 Deposited 2023-10-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded X0L 4-[(4-methylphenyl)methyl]-1~{H}-quinoxaline-2,3-dione × 6 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 1.88 Å R-free 0.215
8QV1 Hexameric HIV-1 CA in complex with DDD01728505 Deposited 2023-10-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded X0H methyl 2-(2-oxidanylidene-1~{H}-quinolin-4-yl)ethanoate × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 2.20 Å R-free 0.288
8QV9 Hexameric HIV-1 CA in complex with DDD01829021 Deposited 2023-10-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded WZL 7-bromanyl-3-(phenylmethyl)-1~{H}-benzimidazol-2-one × 6 EDO 1,2-ETHANEDIOL × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 1.76 Å R-free 0.246
8QVA Hexameric HIV-1 CA in complex with DDD01829894 Deposited 2023-10-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded EDO 1,2-ETHANEDIOL × 12 WZ9 7-azanyl-3-(phenylmethyl)-1~{H}-benzimidazol-2-one × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Resolution 2.00 Å R-free 0.254
8TY6 Disulfide-stabilized HIV-1 CA hexamer in complex with PQBP1 Nt Deposited 2023-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8V17 HIV-CA Disulfide linked Hexamer with inhibitor bound - exploration of a benzothiazole Deposited 2023-11-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–361（229 aa）
Mutation：A14C, E45C, W184A, M185A Y4X N-(1,3-benzothiazol-5-yl)-3,5-difluoro-Nalpha-[(5-hydroxy-1H-indol-3-yl)acetyl]-N-methyl-L-phenylalaninamide × 6 GOL GLYCEROL × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Morpheus Condition D11
Resolution 1.50 Å R-free 0.171
8VRP HIV-CA Disulfide linked Hexamer bound to 4-Quinazolinone Scaffold inhibitor Deposited 2024-01-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain B 133–361（229 aa）
Chain C 133–361（229 aa）
Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A A1ADQ N-[(1S)-1-[(3P,7M)-3-{4-chloro-3-[(ethanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-7-(3-fluoro-4-formylphenyl)-4-oxo-3,4-dihydroquinazolin-2-yl]-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-5,6-dihydrocyclopenta[c]pyrazol-1(4H)-yl]acetamide × 6 IOD IODIDE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Morpheus condition B2
Resolution 1.80 Å R-free 0.226
8VRP HIV-CA Disulfide linked Hexamer bound to 4-Quinazolinone Scaffold inhibitor Deposited 2024-01-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–361（229 aa）
Mutation：A14C, E45C, W184A, M185A A1ADQ N-[(1S)-1-[(3P,7M)-3-{4-chloro-3-[(ethanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-7-(3-fluoro-4-formylphenyl)-4-oxo-3,4-dihydroquinazolin-2-yl]-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-5,6-dihydrocyclopenta[c]pyrazol-1(4H)-yl]acetamide × 6 IOD IODIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Morpheus condition B2
Resolution 1.80 Å R-free 0.226
9D6D Gag CA-SP1 immature lattice bound with Lenacapavir from enveloped virus like particles Deposited 2024-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain B 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain C 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain D 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain E 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain F 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain G 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain H 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain I 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain J 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain K 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain L 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain M 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain N 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain O 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain P 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain Q 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain R 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I QNG Lenacapavir × 18 IHP INOSITOL HEXAKISPHOSPHATE × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；This is the final buffer in which the enveloped viral like particle was resuspended. The Gag-CA-SP1 lattice is inside the viral like particle and thus not in the direct environment of this buffer.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.18 Å
9D6E Gag CA-SP1 immature lattice bound with Bevirimat from enveloped virus like particles Deposited 2024-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain B 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain C 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain D 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain E 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain F 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain G 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain H 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain I 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain J 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain K 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain L 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain M 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain N 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain O 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain P 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain Q 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain R 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I IHP INOSITOL HEXAKISPHOSPHATE × 1 2I4 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；This is the final buffer in which the enveloped viral like particle was resuspended. The Gag-CA-SP1 lattice is inside the viral like particle and thus not in the direct environment of this buffer.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
9D88 Gag CA-SP1 immature lattice from enveloped and perforated virus like particles Deposited 2024-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain B 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain C 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain D 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain E 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain F 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain G 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain H 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain I 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain J 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain K 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain L 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain M 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain N 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain O 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain P 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain Q 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Chain R 143–371（229 aa） Fragment：CA-SP1 domains (UNP residues 143-372)
Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I Mutation：L231I IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；This is the final buffer in which the enveloped viral-like particle was resuspended. The Gag-CA-SP1 lattice is inside the virus-like particle and not directly in the buffer environment.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
9EDZ HIV CA - GLFG peptide (4 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4 10% PEG 4,000
Resolution 3.00 Å R-free 0.267
9EDZ HIV CA - GLFG peptide (4 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain J 133–363（231 aa）
Chain K 133–363（231 aa）
Chain L 133–363（231 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4 10% PEG 4,000
Resolution 3.00 Å R-free 0.267
9EE0 HIV CA - GLFG peptide (9 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4 10% PEG 4,000
Resolution 3.10 Å R-free 0.255
9EE0 HIV CA - GLFG peptide (9 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain J 133–363（231 aa）
Chain K 133–363（231 aa）
Chain L 133–363（231 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4 10% PEG 4,000
Resolution 3.10 Å R-free 0.255
9EE1 HIV CA - GLFG peptide (43 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4, 10% PEG 4,000
Resolution 3.00 Å R-free 0.261
9EE1 HIV CA - GLFG peptide (43 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain J 133–363（231 aa）
Chain K 133–363（231 aa）
Chain L 133–363（231 aa）
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4, 10% PEG 4,000
Resolution 3.00 Å R-free 0.261
9EE2 HIV CA - FSFG peptide (14 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4, 10% PEG 4,000
Resolution 2.99 Å R-free 0.253
9EE2 HIV CA - FSFG peptide (14 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain J 133–363（231 aa）
Chain K 133–363（231 aa）
Chain L 133–363（231 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4, 10% PEG 4,000
Resolution 2.99 Å R-free 0.253
9EE3 HIV CA - FG peptide (14 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4, 10% PEG 4,000
Resolution 3.10 Å R-free 0.261
9EE3 HIV CA - FG peptide (14 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain J 133–363（231 aa）
Chain K 133–363（231 aa）
Chain L 133–363（231 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4, 10% PEG 4,000
Resolution 3.10 Å R-free 0.261
9EE4 HIV CA - FG peptide (34 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4, 10% PEG 4,000
Resolution 3.10 Å R-free 0.252
9EE4 HIV CA - FG peptide (34 mM) Deposited 2024-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 133–363（231 aa）
Chain H 133–363（231 aa）
Chain I 133–363（231 aa）
Chain J 133–363（231 aa）
Chain K 133–363（231 aa）
Chain L 133–363（231 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM Hepes, pH 7.4, 10% PEG 4,000
Resolution 3.10 Å R-free 0.252
9H1P Mature HIV-1 matrix from MA-SP1 cleavage mutant Deposited 2024-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 2–132（131 aa）
Chain B 433–448（16 aa）
Chain C 2–132（131 aa）
Chain D 433–448（16 aa）
Chain E 2–132（131 aa）
Chain F 433–448（16 aa）
Chain G 2–132（131 aa）
Chain H 433–448（16 aa）
Chain I 2–132（131 aa）
Chain J 433–448（16 aa）
Chain K 2–132（131 aa）
Chain L 433–448（16 aa）
Chain M 2–132（131 aa）
Chain N 433–448（16 aa）
Chain O 2–132（131 aa）
Chain P 433–448（16 aa）
Chain Q 2–132（131 aa）
Chain R 433–448（16 aa）
Chain S 2–132（131 aa）
Chain T 433–448（16 aa）
Chain U 2–132（131 aa）
Chain V 433–448（16 aa）
Chain W 2–132（131 aa）
Chain X 433–448（16 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
9MNM SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly. Deposited 2024-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Not recorded QNG Lenacapavir × 18 IHP INOSITOL HEXAKISPHOSPHATE × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2；25 mM MES, 2mM TCEP, 500 uM LEN
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9MNM SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly. Deposited 2024-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Not recorded QNG Lenacapavir × 3 IHP INOSITOL HEXAKISPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2；25 mM MES, 2mM TCEP, 500 uM LEN
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9MNM SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly. Deposited 2024-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Not recorded QNG Lenacapavir × 3 IHP INOSITOL HEXAKISPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2；25 mM MES, 2mM TCEP, 500 uM LEN
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9P9L Gag CA-SP1 immature lattice bound with Lenacapavir from enveloped virus like particles Deposited 2025-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: 18-meric
Chain A 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain B 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain C 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain D 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain E 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain F 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain G 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain H 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain I 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain J 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain K 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain L 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain M 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain N 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain O 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain P 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain Q 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain R 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Not recorded QNG Lenacapavir × 18 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；This is the final buffer in which the enveloped viral like particle was resuspended. The Gag-CA-SP1 lattice is inside the viral like particle and thus not in the direct environment of this buffer.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.28 Å
9P9M CA-SP1 immature lattice assembled in vitro with inhibitor lenacapavir (dialyzed to 50nM) Deposited 2025-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: 18-meric
Chain A 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain B 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain C 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain D 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain E 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain F 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain G 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain H 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain I 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain J 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain K 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain L 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain M 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain N 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain O 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain P 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain Q 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Chain R 143–371（229 aa） Fragment：Capsid (CA) domain and Spacer Peptide 1 (SP1) region
Not recorded QNG Lenacapavir × 18 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；the initial Lenacapavir concentration is 180uM and CA-SP1 is 90uM upon particle assembly; the assembled particle is then dialyzed in same buffer, but have final Lenacapavir concentration drop to 50nM.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å

70 other PDB entries and 88 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GAG_HV1N5
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–231； UniProt 133–363

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8qv4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8qv4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8qv4
Deposition date deposition_date2023-10-17
Structure title titleHexameric HIV-1 CA in complex with DDD01728503
Keywords keywordsCapsid, Viral protein; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.30 Å
Radius of gyration Rg (electron density) rg_electron22.64 Å
Forward intensity I(0) i010862700.00
Molecular weight molecular_weight24344.0 kDa
Excluded volume excluded_volume30391 ų
Envelope volume envelope_volume39053 ų
Hydration-shell volume shell_volume15724 ų
Envelope diameter envelope_diameter83.0 Å
Shell Rg shell_rg27.63 Å
Envelope Rg envelope_rg22.98 Å
Shape Rg shape_rg22.63 Å
Total Rg total_rg23.39 Å
Total atoms total_atoms1704
Residues n_residues216
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax79.9 Å
Rg (real space) rg_real23.51 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real1.0860e+07
I(0) uncertainty (real space) i0_real_error1.7940e+05
Rg (reciprocal space) rg_reciprocal23.46 Å
I(0) (reciprocal space) i0_reciprocal10860000.0000
Solution quality estimate total_estimate0.7427
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary78.7 Å
Skewness Skewness skewness0.476
Kurtosis Kurtosis kurtosis-0.466
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2423000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.589; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (2)

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9. Files and Curves (10)