9pgu

HIV Capsid Hexamer bound to Compound 40

Method: X-RAY DIFFRACTION D_max: 106.8 Å Quality: EXCELLENT

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

HIV-1 capsid

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 133–363 Chain B； UniProt 133–363 Chain C； UniProt 133–363 Chain D； UniProt 133–363 Chain E； UniProt 133–363 Chain F； UniProt 133–363	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

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 9PGU	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 133–353（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
5MCY The structure of the mature HIV-1 CA pentamer in intact virus particles Deposited 2016-11-10	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 × 20 PDB declaration: eicosameric	Chain A 133–353（221 aa） Chain B 133–353（221 aa） Chain F 133–353（221 aa） Chain G 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） Chain T 133–353（221 aa） Chain Z 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 h 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 8.80 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 ligand/ion Different experimental method 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 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） 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 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） 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 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） 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 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） 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 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） 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 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） 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 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） 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 ligand/ion 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 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） 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa）	Mutation：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 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 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） 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 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） 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 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） 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 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） 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 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） 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–351（219 aa）	Not recorded	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 ligand/ion 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 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） 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 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） 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 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） 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 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa）	Mutation：A14C, 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 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–351（219 aa）	Not recorded	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–351（219 aa）	Not recorded	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 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）	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 133–363（231 aa） 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 ligand/ion 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa） Chain B 133–363（231 aa）	Mutation：A14C, E45C, 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 133–363（231 aa）	Mutation：A14C, E45C, 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–352（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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa）	Mutation：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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa）	Mutation：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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 133–354（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 ligand/ion 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 method 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 method 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 133–363（231 aa）	Mutation：A14C, E45C, Q67H, 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 133–363（231 aa）	Mutation：A14C, E45C, Q67H, 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa） Chain B 133–363（231 aa）	Mutation：A14C, E45C, 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 133–363（231 aa）	Mutation：A14C, E45C, 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa） Chain B 133–363（231 aa）	Mutation：A14C, E45C, 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 133–363（231 aa）	Mutation：A14C, E45C, 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa） Chain B 133–363（231 aa）	Mutation：A14C, E45C, 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 133–363（231 aa）	Mutation：A14C, E45C, 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa） Chain B 133–363（231 aa） Chain C 133–363（231 aa） Chain D 133–363（231 aa） Chain E 133–363（231 aa） Chain F 133–363（231 aa）	Mutation：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 method 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 method 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 method 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 ligand/ion Different experimental method 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 method 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 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	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 ligand/ion Different experimental method 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 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	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 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	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 ligand/ion Different experimental method 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 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	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 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	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 ligand/ion Different experimental method 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 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	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 ligand/ion Different experimental method 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa） Chain B 133–363（231 aa） Chain C 133–363（231 aa） Chain D 133–363（231 aa） Chain E 133–363（231 aa） Chain F 133–363（231 aa）	Mutation：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 method 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 method 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 method 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 ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 ligand/ion Different experimental method 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 method 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 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）	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 133–363（231 aa）	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 35 PDB declaration: 35-meric	Chain A 133–363（231 aa） Chain 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 35 PDB declaration: 35-meric	Chain A 133–363（231 aa） Chain 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 35 PDB declaration: 35-meric	Chain A 133–363（231 aa） Chain 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 35 PDB declaration: 35-meric	Chain A 133–363（231 aa） Chain 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa） Chain B 133–363（231 aa） Chain C 133–363（231 aa） Chain D 133–363（231 aa） Chain E 133–363（231 aa） Chain F 133–363（231 aa）	Mutation：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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 133–363（231 aa） Chain H 133–363（231 aa） Chain I 133–363（231 aa） Chain J 133–363（231 aa） Chain K 133–363（231 aa） Chain L 133–363（231 aa）	Mutation：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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa） Chain B 133–363（231 aa） Chain C 133–363（231 aa） Chain D 133–363（231 aa） Chain E 133–363（231 aa） Chain F 133–363（231 aa）	Mutation：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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 133–363（231 aa） Chain H 133–363（231 aa） Chain I 133–363（231 aa） Chain J 133–363（231 aa） Chain K 133–363（231 aa） Chain L 133–363（231 aa）	Mutation：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 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）	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 133–363（231 aa） Chain H 133–363（231 aa） Chain I 133–363（231 aa） Chain J 133–363（231 aa） Chain K 133–363（231 aa） Chain L 133–363（231 aa）	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
9PGV HIV Capsid Hexamer bound to Compound 24 Deposited 2025-07-08	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）	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 133–363（231 aa） Chain H 133–363（231 aa） Chain I 133–363（231 aa） Chain J 133–363（231 aa） Chain K 133–363（231 aa） Chain L 133–363（231 aa）	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 133–363（231 aa）	Not recorded	IOD IODIDE ION × 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 2–232； UniProt 133–363 Author chain B； PDBConstruct 2–232； UniProt 133–363 Author chain C； PDBConstruct 2–232； UniProt 133–363 Author chain D； PDBConstruct 2–232； UniProt 133–363 Author chain E； PDBConstruct 2–232； UniProt 133–363 Author chain F； PDBConstruct 2–232； UniProt 133–363

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pgu
Deposition date deposition_date	2025-07-08
Structure title title	HIV Capsid Hexamer bound to Compound 40
Keywords keywords	Capsid, p24, HIV-1, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.59 Å
Radius of gyration Rg (electron density) rg_electron	34.85 Å
Forward intensity I(0) i0	585628000.00
Molecular weight molecular_weight	129770.0 kDa
Excluded volume excluded_volume	124840 Å³
Envelope volume envelope_volume	229870 Å³
Hydration-shell volume shell_volume	52918 Å³
Envelope diameter envelope_diameter	109.8 Å
Shell Rg shell_rg	43.06 Å
Envelope Rg envelope_rg	34.36 Å
Shape Rg shape_rg	34.86 Å
Total Rg total_rg	35.26 Å
Total atoms total_atoms	9765
Residues n_residues	1239
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.8 Å
Rg (real space) rg_real	35.38 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	5.8560e+08
I(0) uncertainty (real space) i0_real_error	9.3370e+06
Rg (reciprocal space) rg_reciprocal	35.52 Å
I(0) (reciprocal space) i0_reciprocal	585700000.0000
Solution quality estimate total_estimate	0.9063
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.7 Å
Skewness Skewness skewness	0.070
Kurtosis Kurtosis kurtosis	-0.618
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25080000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.890

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

Unit-cell length a length_a	134.650 Å
Unit-cell length b length_b	134.650 Å
Unit-cell length c length_c	211.840 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	3.360 Å
Low-resolution limit resolution_low	49.280 Å
R factor r_factor	0.2238
R_work r_work	0.2209
R_free r_free	0.2623

Description description	HIV-1 capsid
Molecular weight formula_weight	25592.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9765

HIV Capsid Hexamer bound to Compound 40

1. Protein Identity and Related Structures Protein Identity & Related Structures

HIV-1 capsid

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Human immunodeficiency virus 1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

Description description	;(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 ;
Molecular weight formula_weight	635.5 kDa
Source method src_method	syn
Copy count entity_count	6

fit	/app/data/saxs_computation/pg/9pgu/9pgu.fit
pddf	/app/data/pr_computation/pg/9pgu/9pgu.pr.out
profile	/app/data/saxs_computation/pg/9pgu/9pgu.dat