Gag polyprotein
Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
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 × 18 PDB declaration: octadecameric（18） Consistent with protein copy count | Chain A； UniProt 143–371 Chain B； UniProt 143–371 Chain C； UniProt 143–371 Chain D； UniProt 143–371 Chain E； UniProt 143–371 Chain F； UniProt 143–371 Chain G； UniProt 143–371 Chain H； UniProt 143–371 Chain I； UniProt 143–371 Chain J； UniProt 143–371 Chain K； UniProt 143–371 Chain L； UniProt 143–371 Chain M； UniProt 143–371 Chain N； UniProt 143–371 Chain O； UniProt 143–371 Chain P； UniProt 143–371 Chain Q； UniProt 143–371 Chain R； UniProt 143–371 | Fragment：CA-SP1 domains (UNP residues 143-372) 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 |
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 9D88 | 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 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
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 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 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
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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 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）
|
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 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 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）
|
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 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）
|
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 ligand/ion 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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 ligand/ion 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 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 ligand/ion 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 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）
|
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 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）
|
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 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
133–351（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 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
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 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）
|
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 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 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 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 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 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 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 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 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 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 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 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 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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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）
|
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 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：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 ligand/ion 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 ligand/ion 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 |
| 9EDZ HIV CA - GLFG peptide (4 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 | 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 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 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 | 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 ligand/ion 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 ligand/ion 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 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 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 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 ligand/ion 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 ligand/ion 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 1–229； UniProt 143–371 Author chain B； PDBConstruct 1–229； UniProt 143–371 Author chain C； PDBConstruct 1–229； UniProt 143–371 Author chain D； PDBConstruct 1–229； UniProt 143–371 Author chain E； PDBConstruct 1–229； UniProt 143–371 Author chain F； PDBConstruct 1–229； UniProt 143–371 Author chain G； PDBConstruct 1–229； UniProt 143–371 Author chain H； PDBConstruct 1–229； UniProt 143–371 Author chain I； PDBConstruct 1–229； UniProt 143–371 Author chain J； PDBConstruct 1–229； UniProt 143–371 Author chain K； PDBConstruct 1–229； UniProt 143–371 Author chain L； PDBConstruct 1–229； UniProt 143–371 Author chain M； PDBConstruct 1–229； UniProt 143–371 Author chain N； PDBConstruct 1–229； UniProt 143–371 Author chain O； PDBConstruct 1–229； UniProt 143–371 Author chain P； PDBConstruct 1–229； UniProt 143–371 Author chain Q； PDBConstruct 1–229； UniProt 143–371 Author chain R； PDBConstruct 1–229； UniProt 143–371 |
