HIV-1 capsid protein
Human immunodeficiency virus 1
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 133–363 | Not recorded | No other associated polymer | 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 |
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 6WAP | 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 experimental method Different experimental conditions | 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 method 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 method 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 experimental method Different experimental conditions | 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 experimental method Different experimental conditions | 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 experimental method 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 experimental method 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 experimental method 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 method 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 experimental method 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 experimental method 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 experimental method 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 method 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 experimental method 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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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：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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 experimental conditions | 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 oligomeric state 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）
|
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 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 experimental method 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 method 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 method 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 method 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 oligomeric state 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 method 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 oligomeric state 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）
|
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 oligomeric state 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：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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state 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
133–351（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 |
| 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 experimental conditions | 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 oligomeric state 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）
|
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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state 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）
|
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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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）
|
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 |
| 8QV4 Hexameric HIV-1 CA in complex with DDD01728503 Deposited 2023-10-17 | Different oligomeric state 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）
|
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 |
| 8QV9 Hexameric HIV-1 CA in complex with DDD01829021 Deposited 2023-10-17 | Different oligomeric state 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）
|
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 oligomeric state 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）
|
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 oligomeric state 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 oligomeric state 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
133–361（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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 experimental method 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 experimental method 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 method 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 experimental method 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 method 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 method 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 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 |
