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5mcy

The structure of the mature HIV-1 CA pentamer in intact virus particles

Method: ELECTRON MICROSCOPY Dmax: 239.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein p24

OrganismNot specified

UniProt B6DRA0

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 × 20 PDB declaration: eicosameric（20） Consistent with protein copy count Chain A； UniProt 133–353 Chain B； UniProt 133–353 Chain F； UniProt 133–353 Chain G； UniProt 133–353 Chain M； UniProt 133–353 Chain N； UniProt 133–353 Chain O； UniProt 133–353 Chain P； UniProt 133–353 Chain Q； UniProt 133–353 Chain R； UniProt 133–353 Chain S； UniProt 133–353 Chain T； UniProt 133–353 Chain Z； UniProt 133–353 Chain b； UniProt 133–353 Chain c； UniProt 133–353 Chain d； UniProt 133–353 Chain e； UniProt 133–353 Chain f； UniProt 133–353 Chain g； UniProt 133–353 Chain h； UniProt 133–353 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE；10nm colloidal gold was added to the sample prior to plunge freezing Resolution 8.80 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 5MCY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5MCX The structure of the mature HIV-1 CA hexamer in intact virus particles Deposited 2016-11-10 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 133–353（221 aa）
Chain B 133–353（221 aa）
Chain C 133–353（221 aa）
Chain D 133–353（221 aa）
Chain E 133–353（221 aa）
Chain F 133–353（221 aa）
Chain G 133–353（221 aa）
Chain I 133–353（221 aa）
Chain J 133–353（221 aa）
Chain K 133–353（221 aa）
Chain L 133–353（221 aa）
Chain N 133–353（221 aa）
Chain O 133–353（221 aa）
Chain P 133–353（221 aa）
Chain Q 133–353（221 aa）
Chain R 133–353（221 aa）
Chain S 133–353（221 aa）
Chain U 133–353（221 aa）
Chain V 133–353（221 aa）
Chain W 133–353（221 aa）
Chain Y 133–353（221 aa）
Chain Z 133–353（221 aa）
Chain b 133–353（221 aa）
Chain c 133–353（221 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；10nm colloidal gold was added to the sample prior to plunge freezing
Resolution 6.80 Å
5UP4 Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM Deposited 2017-02-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain B 133–353（221 aa）
Chain C 133–353（221 aa）
Chain D 133–353（221 aa）
Chain E 133–353（221 aa）
Chain F 133–353（221 aa）
Chain G 133–353（221 aa）
Chain H 133–353（221 aa）
Chain I 133–353（221 aa）
Chain J 133–353（221 aa）
Chain K 133–353（221 aa）
Chain L 133–353（221 aa）
Chain M 133–353（221 aa）
Chain N 133–353（221 aa）
Chain O 133–353（221 aa）
Chain P 133–353（221 aa）
Chain Q 133–353（221 aa）
Chain R 133–353（221 aa）
Chain S 133–353（221 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å
5W4O Structure of the R18A mutant of the HIV-1 capsid protein Deposited 2017-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：residues 133-363
Mutation：R18A IOD IODIDE ION × 54 CL CHLORIDE ION × 42 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.09 Å R-free 0.246
5W4P Structure of the E28A mutant of the HIV-1 capsid protein Deposited 2017-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：residues 133-363
Mutation：E28A IOD IODIDE ION × 72 CL CHLORIDE ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.19 Å R-free 0.246
5W4Q Structure of the R18A/E28A mutant of the HIV-1 capsid protein Deposited 2017-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：residues 133-363
Mutation：R18A, E28A IOD IODIDE ION × 42 CL CHLORIDE ION × 42 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.29 Å R-free 0.245
6AXR Structure of the P122A mutant of the HIV-1 capsid protein 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 homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：UNP residues 133-363
Mutation：P122A IOD IODIDE ION × 48 CL CHLORIDE ION × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.30 Å R-free 0.268
6AXS Structure of the V11I/T58A/P122A mutant of the HIV-1 capsid protein 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 homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：UNP residues 133-363
Mutation：V11I, T58A, P122A IOD IODIDE ION × 60 CL CHLORIDE ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.40 Å R-free 0.266
6AXT Structure of the T58S/T107I/P122A mutant of the HIV-1 capsid protein 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 homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：UNP residues 133-363
Mutation：T58S, T107I, P122A IOD IODIDE ION × 54 CL CHLORIDE ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, MIB, Glycerol
Resolution 2.40 Å R-free 0.243
6AXV Structure of the T58S/T107I/P122A mutant of the HIV-1 capsid protein in complex with PF-3450074 (PF74) 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 homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：UNP residues 133-363
Mutation：T58S, T107I, P122A IOD IODIDE ION × 30 CL CHLORIDE ION × 54 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 cacosylate, Glycerol
Resolution 2.77 Å R-free 0.279
6AXW Structure of the I124A mutant of the HIV-1 capsid protein 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 homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–362（230 aa） Fragment：UNP residues 133-362
Mutation：I124A IOD IODIDE ION × 54 CL CHLORIDE ION × 60 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, MIB, Glycerol
Resolution 2.40 Å R-free 0.236
6AXX Structure of the T58A/I124A mutant of the HIV-1 capsid protein 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 homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：UNP residues 133-363
Mutation：T58A, I124A IOD IODIDE ION × 48 CL CHLORIDE ION × 54 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, MIB, Glycerol
Resolution 2.60 Å R-free 0.246
6AXY Structure of the V11I/T58A/I124A mutant of the HIV-1 capsid protein 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 homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：V11I, T58A, I124A IOD IODIDE ION × 42 CL CHLORIDE ION × 54 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.78 Å R-free 0.260
6AY9 Structure of the native full-length HIV-1 capsid protein in complex with CPSF6 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） Fragment：UNP residues 133-363
Not recorded IOD IODIDE ION × 36 CL CHLORIDE ION × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.50 Å R-free 0.273
6B2G P38A mutant of HIV-1 capsid protein Deposited 2017-09-20 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） Fragment：UNP residues 133-363
Mutation：P38A IOD IODIDE ION × 48 CL CHLORIDE ION × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, MIB, Glycerol
Resolution 2.41 Å R-free 0.258
6B2H P38A/T216I mutant of the HIV-1 capsid protein Deposited 2017-09-20 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） Fragment：UNP residues 133-363
Mutation：P38A, T216I IOD IODIDE ION × 36 CL CHLORIDE ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.60 Å R-free 0.241
6B2I E45A mutant of the HIV-1 capsid protein Deposited 2017-09-20 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） Fragment：UNP residues 133-363
Mutation：E45A IOD IODIDE ION × 18 CL CHLORIDE ION × 72 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.50 Å R-free 0.250
6B2J E45A mutant of HIV-1 capsid protein (other crystal form) Deposited 2017-09-20 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） Fragment：UNP residues 133-363
Mutation：E45A IOD IODIDE ION × 60 CL CHLORIDE ION × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, MIB, Glycerol
Resolution 2.21 Å R-free 0.223
6B2K E45A/R132T mutant of HIV-1 capsid protein Deposited 2017-09-20 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） Fragment：UNP residues 133-363
Mutation：E45A, R132T IOD IODIDE ION × 48 CL CHLORIDE ION × 42 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, Sodium cacodylate, Glycerol
Resolution 2.00 Å R-free 0.218
6ERM HIV Hexamer with ligand Deposited 2017-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–351（219 aa）
Not recorded AZT 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；277 K；PEG4K
Resolution 2.00 Å R-free 0.235
6ERN HIV Hexamer with ligand Deposited 2017-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 139–351（213 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；277 K；PEG4K
Resolution 2.36 Å R-free 0.237
6MQA Structure of HIV-1 CA P207S Deposited 2018-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：UNP residues 133-363
Mutation：P207S IOD IODIDE ION × 18 CL CHLORIDE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；15% PEG3350, 0.1 M sodium iodide, 0.1 M Bis-Tris propane
Resolution 3.20 Å R-free 0.219
6MQO Structure of HIV-1 CA G208R Deposited 2018-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：UNP residues 133-363
Mutation：G208R IOD IODIDE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 6.5；293 K；15% PEG3350, 0.1 M sodium iodide, Bis-Tris propane, pH 6.5
Resolution 3.20 Å R-free 0.271
6MQP Structure of HIV-1 CA T210K Deposited 2018-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa） Fragment：UNP residues 133-363
Mutation：T210K IOD IODIDE ION × 12 CL CHLORIDE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 5.8；293 K；15% PEG3350, 0.1 M sodium iodide, 0.1 M sodium cacodylate
Resolution 3.30 Å R-free 0.240
6OBH Structure of HIV-1 CA 1/2-hexamer Deposited 2019-03-20 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 × 6 PDB declaration: hexameric
Chain B 133–363（231 aa） Fragment：UNP residues 133-363
Chain E 133–363（231 aa） Fragment：UNP residues 133-363
Mutation：E45C, T54C, W184A, M185A Mutation：E45C, T54C, W184A, M185A NA SODIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 8；293 K；0.1 M PCB buffer, pH 8 (sodium propionate, sodium cacodylate, Bis-Tris propane), 25% w/v PEG1500
Resolution 2.96 Å R-free 0.265
6OMT HIV-1 capsid hexamer R18D mutant Deposited 2019-04-19 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）
Mutation：A14C, E45C, W184A, M185A, R18D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；293.15 K；0.1 M Tris-HCl, pH 8.5, 8% PEG8000
Resolution 2.05 Å R-free 0.221
6PU1 Cysteine stabilized hexameric HIV-1 CA in complex with SEC24C peptide Deposited 2019-07-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 133–363（231 aa）
Mutation：A14C, E45C, W184A, M185A IOD IODIDE ION × 18 CL CHLORIDE ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；12% PEG3350, 24% glycerol, 0.35 M NaI, 50 mM sodium cacodylate pH 6.5
Resolution 2.28 Å R-free 0.272
6R6Q HIV capsid hexamer with IP5 ligand Deposited 2019-03-27 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 133–351（219 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；293 K；PEG 6K, 0.1M NaCl
Resolution 2.73 Å R-free 0.289
6R8C HIV capsid hexamer with IP5 ligand Deposited 2019-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–351（219 aa）
Not recorded 5MY MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；270 K；PEG 6K, 1M NaCl
Resolution 1.92 Å R-free 0.234
6V2F Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, GS-6207 Deposited 2019-11-22 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 A 133–363（231 aa）
Chain B 133–363（231 aa）
Not recorded QNG Lenacapavir × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；298 K；12% PEG 3350, 0.2 M sodium thiocyanate, 0.1 M sodium cacodylate, pH 6.7
Resolution 2.00 Å R-free 0.251
6V2F Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, GS-6207 Deposited 2019-11-22 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 C 133–363（231 aa）
Chain D 133–363（231 aa）
Not recorded QNG Lenacapavir × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；298 K；12% PEG 3350, 0.2 M sodium thiocyanate, 0.1 M sodium cacodylate, pH 6.7
Resolution 2.00 Å R-free 0.251
6V2F Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, GS-6207 Deposited 2019-11-22 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 × 6 PDB declaration: hexameric
Chain E 133–363（231 aa）
Chain F 133–363（231 aa）
Not recorded QNG Lenacapavir × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；298 K；12% PEG 3350, 0.2 M sodium thiocyanate, 0.1 M sodium cacodylate, pH 6.7
Resolution 2.00 Å R-free 0.251
6VKV Co-crystal structure of GS-6207 bound to HIV-1 capsid hexamer Deposited 2020-01-22 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 A 133–363（231 aa）
Chain B 133–363（231 aa）
Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A QNG Lenacapavir × 6 IOD IODIDE ION × 12 CL CHLORIDE ION × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.125-0.35M Sodium Iodide, 3-12% Peg 3350, 6% glycerol, 0.1M sodium cacodylate pH 6.5
Resolution 2.22 Å R-free 0.269
6VKV Co-crystal structure of GS-6207 bound to HIV-1 capsid hexamer Deposited 2020-01-22 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 C 133–363（231 aa）
Mutation：A14C, E45C, W184A, M185A QNG Lenacapavir × 6 IOD IODIDE ION × 6 CL CHLORIDE ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.125-0.35M Sodium Iodide, 3-12% Peg 3350, 6% glycerol, 0.1M sodium cacodylate pH 6.5
Resolution 2.22 Å R-free 0.269
6VWS Hexamer of Helical HIV capsid by RASTR method Deposited 2020-02-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–352（220 aa）
Chain B 133–352（220 aa）
Chain C 133–352（220 aa）
Chain D 133–352（220 aa）
Chain M 133–352（220 aa）
Chain N 133–352（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；1M NaCl, 50mM Tris pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.08 Å
7MKC N74D mutant of the HIV-1 capsid protein in complex with PF-3450074 (PF74) Deposited 2021-04-23 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：N74D 1B0 N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE × 6 IOD IODIDE ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, NaI, Sodium Cacodylate, Glycerol
Resolution 2.65 Å R-free 0.242
7MN0 N74D mutant of the HIV-1 capsid protein Deposited 2021-04-30 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：N74D IOD IODIDE ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, NaI, Sodium Cacodylate, Glycerol
Resolution 2.90 Å R-free 0.274
7N9U CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions Deposited 2021-06-18 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 133–354（222 aa） Fragment：UNP residues 133-354
Chain B 133–354（222 aa） Fragment：UNP residues 133-354
Chain C 133–354（222 aa） Fragment：UNP residues 133-354
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；295 K；0.1 M Bis-Tris propane:HCl, pH 7.0, 1.4 M sodium malonate, pH 7.0
Resolution 3.19 Å R-free 0.258
7N9V CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions Deposited 2021-06-18 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 133–354（222 aa） Fragment：UNP residues 133-354
Chain C 133–354（222 aa） Fragment：UNP residues 133-354
Chain D 133–354（222 aa） Fragment：UNP residues 133-354
Chain G 133–354（222 aa） Fragment：UNP residues 133-354
Chain I 133–354（222 aa） Fragment：UNP residues 133-354
Chain K 133–354（222 aa） Fragment：UNP residues 133-354
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；297 K；potassium nitrate, pH 6.9, 20% PEG3350
Resolution 3.45 Å R-free 0.258
7N9X CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions Deposited 2021-06-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain AAA 133–354（222 aa） Fragment：UNP residues 133-354
Chain BBB 133–354（222 aa） Fragment：UNP residues 133-354
Chain CCC 133–354（222 aa） Fragment：UNP residues 133-354
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；295 K；100 mM Bis-Tris propane, pH 6.8, 15% PEG3350, 200 mM sodium
Resolution 3.51 Å R-free 0.270
7OVQ Immature HIV-1 matrix structure Deposited 2021-06-15 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 2–116（115 aa）
Chain B 2–116（115 aa）
Chain C 2–116（115 aa）
Chain D 2–116（115 aa）
Chain E 2–116（115 aa）
Chain F 2–116（115 aa）
Chain I 2–116（115 aa）
Chain K 2–116（115 aa）
Chain M 2–116（115 aa）
Chain O 2–116（115 aa）
Chain P 2–116（115 aa）
Chain Q 2–116（115 aa）
Chain R 2–116（115 aa）
Chain S 2–116（115 aa）
Chain X 2–116（115 aa）
Chain Y 2–116（115 aa）
Chain Z 2–116（115 aa）
Chain b 2–116（115 aa）
Chain c 2–116（115 aa）
Chain d 2–116（115 aa）
Chain f 2–116（115 aa）
Chain h 2–116（115 aa）
Chain l 2–116（115 aa）
Chain m 2–116（115 aa）
Not recorded MYR MYRISTIC ACID × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7OVR Mature HIV-1 matrix structure Deposited 2021-06-15 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 2–116（115 aa）
Chain B 2–116（115 aa）
Chain C 2–116（115 aa）
Chain D 2–116（115 aa）
Chain E 2–116（115 aa）
Chain F 2–116（115 aa）
Chain H 2–116（115 aa）
Chain I 2–116（115 aa）
Chain J 2–116（115 aa）
Chain O 2–116（115 aa）
Chain P 2–116（115 aa）
Chain Q 2–116（115 aa）
Chain R 2–116（115 aa）
Chain S 2–116（115 aa）
Chain U 2–116（115 aa）
Chain W 2–116（115 aa）
Chain Y 2–116（115 aa）
Chain b 2–116（115 aa）
Chain c 2–116（115 aa）
Chain d 2–116（115 aa）
Chain e 2–116（115 aa）
Chain f 2–116（115 aa）
Chain j 2–116（115 aa）
Chain l 2–116（115 aa）
Not recorded MYR MYRISTIC ACID × 24 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
7RHM Structure of Q67H/N74D mutant of disulfide stabilized HIV-1 CA hexamer 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, N74D, W184A, M185A, IOD IODIDE ION × 24 CL CHLORIDE ION × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.35M NaI, 3% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5
Resolution 2.16 Å R-free 0.260
7RJ2 Co-crystal structure of lenacapavir bound to Q67H/N74D mutant of disulfide stabilized HIV-1 CA hexamer Deposited 2021-07-20 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, N74D, W184A, M185A QNG Lenacapavir × 6 CL CHLORIDE ION × 24 IOD IODIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.425M NaI, 6% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5
Resolution 2.32 Å R-free 0.246
7RJ4 Co-crystal structure of lenacapavir bound to N74D mutant of disulfide stabilized HIV-1 CA hexamer Deposited 2021-07-20 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, N74D, W184A, M185A Mutation：A14C, E45C, N74D, W184A, M185A QNG Lenacapavir × 6 CL CHLORIDE ION × 36 IOD IODIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.05M NaI, 3% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5
Resolution 3.32 Å R-free 0.331
7RJ4 Co-crystal structure of lenacapavir bound to N74D mutant of disulfide stabilized HIV-1 CA hexamer Deposited 2021-07-20 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, N74D, W184A, M185A QNG Lenacapavir × 6 CL CHLORIDE ION × 36 IOD IODIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.05M NaI, 3% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5
Resolution 3.32 Å R-free 0.331
7RMJ Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor (S)-N-(1-(3-(4-chloro-3-(methylsulfonamido)-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl)-6-(3-methyl-3-(methylsulfonyl)but-1-yn-1-yl)pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl)-2-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl)acetamide Deposited 2021-07-27 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 × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Mutation：A14C, E45C, W184A, M185A Mutation：A14C, E45C, W184A, M185A 61F N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetamide × 6 IOD IODIDE ION × 9 CL CHLORIDE ION × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.125M NaI, 4.5% Peg 3350, 6% glycerol, 0.1M sodium cacodylate pH 6.5
Resolution 2.27 Å R-free 0.248
7RMJ Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor (S)-N-(1-(3-(4-chloro-3-(methylsulfonamido)-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl)-6-(3-methyl-3-(methylsulfonyl)but-1-yn-1-yl)pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl)-2-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl)acetamide Deposited 2021-07-27 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, W184A, M185A 61F N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetamide × 6 IOD IODIDE ION × 12 CL CHLORIDE ION × 42 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.125M NaI, 4.5% Peg 3350, 6% glycerol, 0.1M sodium cacodylate pH 6.5
Resolution 2.27 Å R-free 0.248
7RMM Structure of N74D mutant of disulfide stabilized HIV-1 CA hexamer Deposited 2021-07-27 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 × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Mutation：A14C, E45C, N74D, W184A, M185A Mutation：A14C, E45C, N74D, W184A, M185A IOD IODIDE ION × 12 CL CHLORIDE ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2M NaI, 5% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5
Resolution 1.97 Å R-free 0.246
7RMM Structure of N74D mutant of disulfide stabilized HIV-1 CA hexamer Deposited 2021-07-27 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, N74D, W184A, M185A IOD IODIDE ION × 12 CL CHLORIDE ION × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2M NaI, 5% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5
Resolution 1.97 Å R-free 0.246
7T13 Hexameric HIV-1 (M-group) CA Q50Y mutant Deposited 2021-12-01 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, Q50Y, W184A, M185A Mutation：A14C, E45C, Q50Y, W184A, M185A Mutation：A14C, E45C, Q50Y, W184A, M185A Mutation：A14C, E45C, Q50Y, W184A, M185A Mutation：A14C, E45C, Q50Y, W184A, M185A Mutation：A14C, E45C, Q50Y, W184A, M185A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；Crystallant: 19% (v/v) PEG 550MME, 100 mM TRIS (pH 8.0), 150 mM KSCN, 10 mM ATP, 3% (v/v) 3,5-hexanediol. Crystals grew in 2 ul protein (13 mg/ml) + 2 ul crystallant. Cryoprotected in 20% (v/v) MPD
Resolution 3.15 Å R-free 0.239
7URT T=1 particle HIV-1 CA G60A/G61P/M66A 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 × 60 PDB declaration: 60-meric
Chain A 133–363（231 aa）
Mutation：G60A/G61P/M66a IHP INOSITOL HEXAKISPHOSPHATE × 120 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.39 Å
7URT T=1 particle HIV-1 CA G60A/G61P/M66A Deposited 2022-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–363（231 aa）
Mutation：G60A/G61P/M66a IHP INOSITOL HEXAKISPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.39 Å
7URT T=1 particle HIV-1 CA G60A/G61P/M66A Deposited 2022-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 133–363（231 aa）
Mutation：G60A/G61P/M66a IHP INOSITOL HEXAKISPHOSPHATE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.39 Å
7URT T=1 particle HIV-1 CA G60A/G61P/M66A Deposited 2022-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：G60A/G61P/M66a IHP INOSITOL HEXAKISPHOSPHATE × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.39 Å
7URT T=1 particle HIV-1 CA G60A/G61P/M66A Deposited 2022-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–363（231 aa）
Mutation：G60A/G61P/M66a IHP INOSITOL HEXAKISPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.39 Å
8CKV HIV-1 mature capsid hexamer from CA-IP6 CLPs Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state 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 No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8CKW HIV-1 mature capsid pentamer from CA-IP6 CLPs Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8CKX HIV-1 mature capsid hexamer next to pentamer (type I) from CA-IP6 CLPs Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state 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）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
8CKY HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to Nup153 peptide Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state 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 No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8CKZ HIV-1 mature capsid pentamer from CA-IP6 CLPs bound to Nup153 peptide Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8CL0 HIV-1 mature capsid hexamer next to pentamer (type I) from CA-IP6 CLPs bound to Nup153 peptide. Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state 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 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8CL1 HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to CPSF6 peptide. Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state 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 No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8CL2 HIV-1 mature capsid pentamer from CA-IP6 CLPs bound to CPSF6 peptide Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8CL3 HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to Sec24C peptide. Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state 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 No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
8CL4 HIV-1 mature capsid pentamer from CA-IP6 CLPs bound to Sec24C peptide Deposited 2023-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
8D3B Hexameric HIV-1 (M-group) Q50Y/R120 mutant Deposited 2022-06-01 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：Q50Y, R120(insertion), A14C, E45C, W185A, M186A Mutation：Q50Y, R120(insertion), A14C, E45C, W185A, M186A Mutation：Q50Y, R120(insertion), A14C, E45C, W185A, M186A Mutation：Q50Y, R120(insertion), A14C, E45C, W185A, M186A Mutation：Q50Y, R120(insertion), A14C, E45C, W185A, M186A Mutation：Q50Y, R120(insertion), A14C, E45C, W185A, M186A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；20% PEG550MME, 0.1M TRIS (pH 8.0), 0.15M KSCN, 10mM ATP, 3% EtOH
Resolution 3.30 Å R-free 0.275
8EEP T=1 particle HIV-1 CA G60A/G61P Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric
Chain A 133–363（231 aa）
Mutation：G60A, G61P IHP INOSITOL HEXAKISPHOSPHATE × 120 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.20 Å
8EEP T=1 particle HIV-1 CA G60A/G61P Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–363（231 aa）
Mutation：G60A, G61P IHP INOSITOL HEXAKISPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.20 Å
8EEP T=1 particle HIV-1 CA G60A/G61P Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 133–363（231 aa）
Mutation：G60A, G61P IHP INOSITOL HEXAKISPHOSPHATE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.20 Å
8EEP T=1 particle HIV-1 CA G60A/G61P Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：G60A, G61P IHP INOSITOL HEXAKISPHOSPHATE × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.20 Å
8EEP T=1 particle HIV-1 CA G60A/G61P Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–363（231 aa）
Mutation：G60A, G61P IHP INOSITOL HEXAKISPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 2.20 Å
8EET T=1 particle HIV-1 CA M66A Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric
Chain A 133–363（231 aa）
Mutation：M66A IHP INOSITOL HEXAKISPHOSPHATE × 120 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 3.10 Å
8EET T=1 particle HIV-1 CA M66A Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–363（231 aa）
Mutation：M66A IHP INOSITOL HEXAKISPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 3.10 Å
8EET T=1 particle HIV-1 CA M66A Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 133–363（231 aa）
Mutation：M66A IHP INOSITOL HEXAKISPHOSPHATE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 3.10 Å
8EET T=1 particle HIV-1 CA M66A Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Mutation：M66A IHP INOSITOL HEXAKISPHOSPHATE × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 3.10 Å
8EET T=1 particle HIV-1 CA M66A Deposited 2022-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–363（231 aa）
Mutation：M66A IHP INOSITOL HEXAKISPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge-freezing
Resolution 3.10 Å
8FIU Potent long-acting inhibitors targeting HIV-1 capsid based on a versatile quinazolin-4-one scaffold Deposited 2022-12-16 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）
Chain B 133–363（231 aa）
Not recorded EDO 1,2-ETHANEDIOL × 15 Y05 N-[(1S)-1-{(3P)-3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl}-7-[(2R,6S)-2,6-dimethylmorpholin-4-yl]-4-oxo-3,4-dihydroquinazolin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；294 K；100 mM bicine, pH 9.0 and 14% (w/v) PEG3350
Resolution 1.56 Å R-free 0.194
8FIU Potent long-acting inhibitors targeting HIV-1 capsid based on a versatile quinazolin-4-one scaffold Deposited 2022-12-16 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）
Not recorded EDO 1,2-ETHANEDIOL × 12 Y05 N-[(1S)-1-{(3P)-3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl}-7-[(2R,6S)-2,6-dimethylmorpholin-4-yl]-4-oxo-3,4-dihydroquinazolin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；294 K；100 mM bicine, pH 9.0 and 14% (w/v) PEG3350
Resolution 1.56 Å R-free 0.194
8G6K HIV-1 CA lattice bound to IP6; from capsid-like particles Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state 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 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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8G6K HIV-1 CA lattice bound to IP6; from capsid-like particles Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8G6K HIV-1 CA lattice bound to IP6; from capsid-like particles Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8G6L HIV-1 capsid lattice bound to IP6, pH 6.2 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state 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 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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8G6L HIV-1 capsid lattice bound to IP6, pH 6.2 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8G6L HIV-1 capsid lattice bound to IP6, pH 6.2 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8G6M HIV-1 CA lattice bound to IP6, pH 7.4 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state 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 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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G6M HIV-1 CA lattice bound to IP6, pH 7.4 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G6M HIV-1 CA lattice bound to IP6, pH 7.4 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G6N HIV-1 capsid lattice bound to dNTPs Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state 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 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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8G6N HIV-1 capsid lattice bound to dNTPs Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8G6N HIV-1 capsid lattice bound to dNTPs Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric
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）
Chain G 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8G6O HIV-1 capsid lattice bound to IP6 and Lenacapavir Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 25 PDB declaration: 25-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）
Chain E 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G6O HIV-1 capsid lattice bound to IP6 and Lenacapavir Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
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）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G6O HIV-1 capsid lattice bound to IP6 and Lenacapavir Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
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）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TQP HIV-CA Disulfide linked Hexamer bound to Quinazolin-4-one Scaffold inhibitor Deposited 2023-08-08 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：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A K3L 2-[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]-N-{(1R)-2-(3,5-difluorophenyl)-1-[3-(4-methoxyphenyl)-4-oxo-3,4-dihydroquinazolin-2-yl]ethyl}acetamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PACT E4
Resolution 2.90 Å R-free 0.247
8TQP HIV-CA Disulfide linked Hexamer bound to Quinazolin-4-one Scaffold inhibitor Deposited 2023-08-08 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：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A Mutation：A14C, E45C, W184A, M184A K3L 2-[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]-N-{(1R)-2-(3,5-difluorophenyl)-1-[3-(4-methoxyphenyl)-4-oxo-3,4-dihydroquinazolin-2-yl]ethyl}acetamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PACT E4
Resolution 2.90 Å R-free 0.247
9PGS HIV Capsid Hexamer bound to Compound 6 Deposited 2025-07-08 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：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 A1CH4 3,5-difluoro-Nalpha-[(5-hydroxy-1H-indol-3-yl)acetyl]-N-(4-methoxyphenyl)-N-methyl-L-phenylalaninamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；30% PEG 8000, 0.1M sodium malonate
Resolution 2.40 Å R-free 0.261
9PGS HIV Capsid Hexamer bound to Compound 6 Deposited 2025-07-08 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：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 A1CH4 3,5-difluoro-Nalpha-[(5-hydroxy-1H-indol-3-yl)acetyl]-N-(4-methoxyphenyl)-N-methyl-L-phenylalaninamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；30% PEG 8000, 0.1M sodium malonate
Resolution 2.40 Å R-free 0.261
9PGT HIV Capsid Hexamer bound to Compound 12 Deposited 2025-07-08 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）
Not recorded A1CH5 N-[(1S)-1-[3-(4-chlorophenyl)pyridin-2-yl]-2-(3,5-difluorophenyl)ethyl]-2-(5-hydroxy-1H-indol-3-yl)acetamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；12% PEG 8K, 0.1M sodium malonate
Resolution 2.20 Å R-free 0.247
9PGT HIV Capsid Hexamer bound to Compound 12 Deposited 2025-07-08 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）
Not recorded A1CH5 N-[(1S)-1-[3-(4-chlorophenyl)pyridin-2-yl]-2-(3,5-difluorophenyl)ethyl]-2-(5-hydroxy-1H-indol-3-yl)acetamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；12% PEG 8K, 0.1M sodium malonate
Resolution 2.20 Å R-free 0.247
9PGU HIV Capsid Hexamer bound to Compound 40 Deposited 2025-07-08 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）
Not recorded A1CH6 (5M)-5-{2-[(1S)-2-(3,5-difluorophenyl)-1-{2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamido}ethyl]pyridin-3-yl}-2-fluorobenzamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；7% peg 8000, 0.1M sodium malonate, pH 6.5
Resolution 3.36 Å R-free 0.262
9PGV HIV Capsid Hexamer bound to Compound 24 Deposited 2025-07-08 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）
Not recorded A1CH7 N-methyl-N-phenyl-3-(pyridin-3-yl)-N~2~-{[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}-L-alaninamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；12% PEG 8000, 100 mM sodium malonate
Resolution 2.30 Å R-free 0.263
9PGV HIV Capsid Hexamer bound to Compound 24 Deposited 2025-07-08 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）
Not recorded A1CH7 N-methyl-N-phenyl-3-(pyridin-3-yl)-N~2~-{[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}-L-alaninamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；12% PEG 8000, 100 mM sodium malonate
Resolution 2.30 Å R-free 0.263
9S6W HIV-1 capsid (M-group) - native in complex with JW3-100 Deposited 2025-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Not recorded IOD IODIDE ION × 12 CL CHLORIDE ION × 24 BME BETA-MERCAPTOETHANOL × 6 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL × 6 A1JL5 (S)-N-(1-(5-((2-amino-2-oxoethyl)thio)-4-(4-(tert-Butyl)phenyl)-4H-1,2,4-triazol-3-yl)-2-(3,5-difluorophenyl)ethyl)-2-(5-hydroxy-1H-indol-3-yl)acetamide × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9.5-11% PEG 3350 (v/v), 250-350 mM NaI, 100 mM Sodium Cacodylate [pH 6.5]. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.
Resolution 2.07 Å R-free 0.298

70 other PDB entries and 103 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B6DRA0_9HIV1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–221； UniProt 133–353 Author chain B； PDBConstruct 1–221； UniProt 133–353 Author chain F； PDBConstruct 1–221； UniProt 133–353 Author chain G； PDBConstruct 1–221； UniProt 133–353 Author chain M； PDBConstruct 1–221； UniProt 133–353 Author chain N； PDBConstruct 1–221； UniProt 133–353 Author chain O； PDBConstruct 1–221； UniProt 133–353 Author chain P； PDBConstruct 1–221； UniProt 133–353 Author chain Q； PDBConstruct 1–221； UniProt 133–353 Author chain R； PDBConstruct 1–221； UniProt 133–353 Author chain S； PDBConstruct 1–221； UniProt 133–353 Author chain T； PDBConstruct 1–221； UniProt 133–353 Author chain Z； PDBConstruct 1–221； UniProt 133–353 Author chain b； PDBConstruct 1–221； UniProt 133–353 Author chain c； PDBConstruct 1–221； UniProt 133–353 Author chain d； PDBConstruct 1–221； UniProt 133–353 Author chain e； PDBConstruct 1–221； UniProt 133–353 Author chain f； PDBConstruct 1–221； UniProt 133–353 Author chain g； PDBConstruct 1–221； UniProt 133–353 Author chain h； PDBConstruct 1–221； UniProt 133–353

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

SAXS scattering curve SAXS Profile

SAXS profile for 5mcy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5mcy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5mcy
Deposition date deposition_date2016-11-10
Structure title titleThe structure of the mature HIV-1 CA pentamer in intact virus particles
Keywords keywordsretrovirus, HIV-1, capsid, pentamer, viral protein; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier68.04 Å
Radius of gyration Rg (electron density) rg_electron68.05 Å
Forward intensity I(0) i02291860000.00
Molecular weight molecular_weight247370.0 kDa
Excluded volume excluded_volume242810 ų
Envelope volume envelope_volume875530 ų
Hydration-shell volume shell_volume109480 ų
Envelope diameter envelope_diameter228.0 Å
Shell Rg shell_rg65.88 Å
Envelope Rg envelope_rg65.11 Å
Shape Rg shape_rg68.04 Å
Total Rg total_rg68.01 Å
Total atoms total_atoms17660
Residues n_residues4420
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax239.8 Å
Rg (real space) rg_real67.98 Å
Rg uncertainty (real space) rg_real_error2.54 Å
I(0) (real space) i0_real2.2920e+09
I(0) uncertainty (real space) i0_real_error5.6080e+07
Rg (reciprocal space) rg_reciprocal68.13 Å
I(0) (reciprocal space) i0_reciprocal2292000000.0000
Solution quality estimate total_estimate0.8736
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary83.4 Å
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.463
Angular range angular_range— – 0.1150 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha234800000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.840
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)