9q09

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab76 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664

Method: ELECTRON MICROSCOPY D_max: 170.1 Å Quality: REASONABLE

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

BG505 SOSIP.664 gp120

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	Other combination Heteromer Protein × 18 其他Polymer 44 PDB declaration: octadecameric（18） Consistent with protein copy count	Chain A； UniProt 30–508 Chain B； UniProt 509–661 Chain C； UniProt 509–661 Chain G； UniProt 30–508 Chain I； UniProt 30–508 Chain J； UniProt 509–661	Not recorded	Ab76 Fab heavy chain × 3 Ab76 Fab light chain × 3 PGT121 Fab heavy chain × 3 PGT121 Fab light chain × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 26 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；1X PBS buffer cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.23 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 9Q09	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4TVP Crystal Structure of the HIV-1 BG505 SOSIP.664 Env Trimer Ectodomain, Comprising Atomic-Level Definition of Pre-Fusion gp120 and gp41, in Complex with Human Antibodies PGT122 and 35O22 Deposited 2014-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain B 509–661（153 aa） Fragment：UNP residues 509-661 Chain G 30–505（476 aa） Fragment：UNP residues 30-505	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 SO4 SULFATE ION × 30	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；16% isopropanol, 5.32% PEG1500, 0.2M LiSO4, 0.1M Sodium acetate pH 5.5	Resolution 3.10 Å R-free 0.248
5U7M Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-378806 in Complex with Human Antibodies PGT122 and 35O22 at 3.8 Angstrom Deposited 2016-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 509–661（153 aa） Fragment：UNP residues 509-661 Chain G 30–510（481 aa） Fragment：UNP residues 30-505	Not recorded	SO4 SULFATE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 83G 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；6% ISOPROPANOL, 5.32% PEG1500, 0.2M LISO4, 0.1M SODIUM ACETATE PH 5.5	Resolution 3.02 Å R-free 0.289
5U7O Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-626529 in Complex with Human Antibodies PGT122 and 35O22 at 3.8 Angstrom Deposited 2016-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 509–661（153 aa） Fragment：UNP residues 509-661 Chain G 30–510（481 aa） Fragment：UNP residues 30-510	Not recorded	SO4 SULFATE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 83J 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-[4-methoxy-7-(3-methyl-1H-1,2,4-triazol-1-yl)-1H-pyrrolo[2,3-c]pyridin-3-yl]ethane-1,2-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；16% ISOPROPANOL, 5.32% PEG1500, 0.2M LISO4, 0.1M SODIUM ACETATE PH 5.5	Resolution 3.03 Å R-free 0.325
6CDE Cryo-EM structure at 3.8 A resolution of vaccine-elicited antibody vFP20.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122 Deposited 2018-02-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 24-meric	Chain 2 30–502（473 aa） Chain C 30–502（473 aa） Chain c 30–502（473 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MAN alpha-D-mannopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6CDI Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122 Deposited 2018-02-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 24-meric	Chain 2 30–502（473 aa） Chain C 30–502（473 aa） Chain d 30–502（473 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6CE0 Crystal structure of a HIV-1 clade B tier-3 isolate H078.14 UFO-BG Env trimer in complex with broadly neutralizing Fabs PGT124 and 35O22 at 4.6 Angstrom Deposited 2018-02-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 567–661（95 aa）	Mutation：T602C,T602C,T602C,T602C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277.15 K；0.1 Tris (pH 7.4), 0.2 M lithium sulfate, 6% (w/v) polyethylene glycol 4000	Resolution 4.60 Å R-free 0.341
6CM3 BG505 SOSIP in complex with sCD4, 17b, 8ANC195 Deposited 2018-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 21-meric	Chain D 30–508（479 aa） Chain E 30–508（479 aa） Chain F 30–508（479 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.54 Å
6CRQ Glutaraldehyde-treated BG505 SOSIP.664 Env in complex with PGV04 Fab Deposited 2018-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 31–505（475 aa） Chain B 31–505（475 aa） Chain F 31–505（475 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50 mM Tris, 150 mM NaCl, 0.3 mM DDM. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6DFH BG505 MD64 N332-GT2 SOSIP trimer in complex with germline-reverted BG18 fragment antigen binding Deposited 2018-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 509–661（153 aa） Chain E 509–661（153 aa） Chain F 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；5 second blot time	Resolution 3.85 Å
6UDA Cryo-EM structure of CH235UCA bound to Man5-enriched CH505.N279K.G458Y.SOSIP.664 Deposited 2019-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain F 508–661（154 aa） Chain J 508–661（154 aa） Chain Z 508–661（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6VY2 Cryo-EM structure of M1214_N1 Fab in complex with CH505 TF chimeric SOSIP.664 Env trimer Deposited 2020-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 508–661（154 aa） Chain D 508–661（154 aa） Chain F 508–661（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.86 Å
7KLC Crystal structure of M4H2K1 Fab bound to HIV-1 BG505 gp120 core and to 17b Fab Deposited 2020-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 43–126（84 aa） Fragment：UNP residues 43-126,194-489,UNP residues 43-126,194-489,UNP residues 43-126,194-489,UNP residues 43-126,194-489 Chain A 194–489（296 aa） Fragment：UNP residues 43-126,194-489,UNP residues 43-126,194-489,UNP residues 43-126,194-489,UNP residues 43-126,194-489	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1M Tris, pH 7, 1.825 M ammonium sulfate, 0.29 M lithium sulfate, 15% ethylene glycol	Resolution 4.30 Å R-free 0.334
7L8E BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-1 from animal Rh.33172 (Wk38 time point) Deposited 2020-12-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain B 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain C 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain D 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain E 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain F 30–661（632 aa） Fragment：GP120 domain, residues 30-661	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 44	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；TBS buffer prepared from a 10X stock cryo-EM vitrification conditions Cryogen ETHANE；Blotting time varied between 3 and 7 seconds.	Resolution 4.20 Å
7L8F BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-2 from animal Rh.33172 (Wk38 time point) Deposited 2020-12-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain B 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain C 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain D 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain E 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain F 30–661（632 aa） Fragment：GP120 domain, residues 30-661	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 49	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；TBS buffer prepared from a 10X stock cryo-EM vitrification conditions Cryogen ETHANE；Blotting time varied between 3 and 7 seconds.	Resolution 3.66 Å
7L8G BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-3 from animal Rh.33172 (Wk38 time point) Deposited 2020-12-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain B 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain C 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain D 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain E 30–661（632 aa） Fragment：GP120 domain, residues 30-661 Chain F 30–661（632 aa） Fragment：GP120 domain, residues 30-661	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；TBS buffer prepared from a 10X stock cryo-EM vitrification conditions Cryogen ETHANE；Blotting time varied between 3 and 7 seconds.	Resolution 4.30 Å
7T9T Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with complex glycans Deposited 2021-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 508–661（154 aa） Chain F 508–661（154 aa） Chain J 508–661（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2.5 S before plunging	Resolution 3.70 Å
7TCN Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with high-mannose glycans Deposited 2021-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 508–661（154 aa） Chain F 508–661（154 aa） Chain J 508–661（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 MAN alpha-D-mannopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；BLOT FOR 2.5 S BEFORE PLUNGING	Resolution 4.10 Å
7TCO Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.G458Y.SOSIP.664 with high-mannose glycans Deposited 2021-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 508–661（154 aa） Chain F 508–661（154 aa） Chain N 508–661（154 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；BLOT FOR 2.5 S BEFORE PLUNGING	Resolution 4.19 Å
7UGN Cryo-EM structure of BG24 inferred germline Fabs with germline CDR3s and 10-1074 Fabs in complex with HIV-1 Env immunogen BG505-SOSIPv4.1-GT1 - Class 1 Deposited 2022-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 31–503（473 aa） Chain B 31–503（473 aa） Chain C 31–503（473 aa） Chain D 515–661（147 aa） Chain E 515–661（147 aa） Chain F 515–661（147 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 MAN alpha-D-mannopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7UGO Cryo-EM structure of BG24 inferred germline Fabs with mature CDR3s and 10-1074 Fabs in complex with HIV-1 Env immunogen BG505-SOSIPv4.1-GT1 Deposited 2022-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 31–503（473 aa） Chain B 31–503（473 aa） Chain C 31–503（473 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 MAN alpha-D-mannopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
7UGP Cryo-EM structure of BG24 Fabs with an inferred germline light chain and 10-1074 Fabs in complex with HIV-1 Env immunogen BG505-SOSIPv4.1-GT1 containing the N276 gp120 glycan- Class 1 Deposited 2022-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 31–503（473 aa） Chain B 31–503（473 aa） Chain C 31–503（473 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8C8T cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with bNAbs EPTC112 and 3BNC117 Deposited 2023-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 33–501（469 aa） Chain F 33–501（469 aa） Chain G 33–501（469 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8FYI Structure of HIV-1 BG505 SOSIP-HT1 in complex with one CD4 molecule Deposited 2023-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 32–505（474 aa） Chain B 32–505（474 aa） Chain C 32–505（474 aa）	Mutation：D368R Mutation：D368R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8FYJ Structure of HIV-1 BG505 SOSIP-HT2 in complex with two CD4 molecules (class I) Deposited 2023-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 32–505（474 aa） Chain B 32–505（474 aa） Chain C 32–505（474 aa）	Mutation：D368R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8TKC CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-b.01 FAB Deposited 2023-07-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 30–508（479 aa） Chain B 509–661（153 aa） Chain C 30–508（479 aa） Chain D 509–661（153 aa） Chain E 30–508（479 aa） Chain F 509–661（153 aa）	Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8TL2 CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-c.01 FAB Deposited 2023-07-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain A 30–508（479 aa） Chain B 509–661（153 aa） Chain C 30–508（479 aa） Chain D 509–661（153 aa） Chain E 30–508（479 aa） Chain F 509–661（153 aa）	Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8TL3 CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-d.01 FAB Deposited 2023-07-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 30–508（479 aa） Chain B 509–661（153 aa） Chain C 30–508（479 aa） Chain D 509–661（153 aa） Chain E 30–508（479 aa） Chain F 509–661（153 aa）	Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8TL4 CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-e.01 FAB Deposited 2023-07-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 30–508（479 aa） Chain B 509–661（153 aa） Chain C 30–508（479 aa） Chain D 509–661（153 aa） Chain E 30–508（479 aa） Chain F 509–661（153 aa）	Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8TL5 CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO HERH-c.01 FAB Deposited 2023-07-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 30–508（479 aa） Chain B 509–661（153 aa） Chain C 30–508（479 aa） Chain D 509–661（153 aa） Chain E 30–508（479 aa） Chain F 509–661（153 aa）	Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations Mutation：BG505 DS-SOSIP mutations	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8TNU Cryo-EM structure of TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP Deposited 2023-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain E 30–508（479 aa） Chain F 30–508（479 aa） Chain G 30–508（479 aa） Chain X 509–661（153 aa） Chain Y 509–661（153 aa） Chain Z 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å
8TO7 Cryo-EM structure of HERH-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP Deposited 2023-08-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 509–661（153 aa） Chain B 509–661（153 aa） Chain C 509–661（153 aa） Chain D 30–508（479 aa） Chain E 30–508（479 aa） Chain F 30–508（479 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
8TQ1 HIV-1 BG505 Env SOSIP in complex with bovine Fab Bess4 and non-human primate Fab RM20A3 Deposited 2023-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 13-meric	Chain B 509–661（153 aa） Chain F 509–661（153 aa） Chain K 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8TTW Cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with temsavir, 8ANC195, and 10-1074 Deposited 2023-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain B 509–661（153 aa） Chain F 509–661（153 aa） Chain J 509–661（153 aa）	Mutation：I559P T605C Mutation：I559P T605C Mutation：I559P T605C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 83J 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-[4-methoxy-7-(3-methyl-1H-1,2,4-triazol-1-yl)-1H-pyrrolo[2,3-c]pyridin-3-yl]ethane-1,2-dione × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
8ULR Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 05_B08 Fabs Deposited 2023-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 509–661（153 aa） Chain D 509–661（153 aa） Chain F 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3s blot, 0 blot force	Resolution 3.30 Å
8ULS Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 01_D03 Fabs Deposited 2023-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain B 509–661（153 aa） Chain D 509–661（153 aa） Chain F 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3s blot, 0 blot force	Resolution 3.20 Å
8ULT Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A06 Fabs Deposited 2023-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain B 509–661（153 aa） Chain D 509–661（153 aa） Chain F 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3s blot, 0 blot force	Resolution 3.80 Å
8ULU Cryo-EM structure of the BG505 SOSIPv2 in complex with bNAb 04_A06 and PGDM1400 Fabs Deposited 2023-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 14-meric	Chain B 509–661（153 aa） Chain D 509–661（153 aa） Chain F 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3s blot, 0 blot force	Resolution 3.80 Å
9D7O Cryo-EM structure of BG505 DS-SOSIP.664 with 1 CH103 Fab bound Deposited 2024-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 9–501（493 aa） Chain B 502–661（160 aa） Chain C 9–501（493 aa） Chain D 502–661（160 aa） Chain E 9–501（493 aa） Chain F 502–661（160 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2	Resolution 3.56 Å
9D8V Cryo-EM structure of the BG505 SOSIPv2 Deposited 2024-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 32–501（470 aa） Fragment：UNP residues 32-501 Chain B 516–661（146 aa） Fragment：UNP residues 516-661 Chain C 32–501（470 aa） Fragment：UNP residues 32-501 Chain D 516–661（146 aa） Fragment：UNP residues 516-661 Chain E 32–501（470 aa） Fragment：UNP residues 32-501 Chain F 516–661（146 aa） Fragment：UNP residues 516-661	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3s blot, 0 blot force	Resolution 2.90 Å
9D8Y Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with one gp120 rotated, Population 4 Deposited 2024-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 32–500（469 aa） Chain B 32–500（469 aa） Chain C 32–500（469 aa）	Mutation：T332N, A501C Mutation：T332N, A501C Mutation：T332N, A501C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.06 Å
9D90 Cryo-EM structure of partially open HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-17b Fab and 3-VRC34.01 Fab, Population 1 Deposited 2024-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 21-meric	Chain A 32–500（469 aa） Chain B 32–500（469 aa） Chain C 32–500（469 aa） Chain D 509–657（149 aa） Chain E 509–657（149 aa） Chain F 509–657（149 aa）	Mutation：T332N, A501C Mutation：T332N, A501C Mutation：T332N, A501C Mutation：I559P, T605C Mutation：I559P, T605C Mutation：I559P, T605C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å
9D98 Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with two gp120 protomers rotated, Population 5 Deposited 2024-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 32–500（469 aa） Chain B 32–500（469 aa） Chain C 32–500（469 aa） Chain D 509–661（153 aa） Chain E 509–661（153 aa） Chain F 509–661（153 aa）	Mutation：T332N, A501C Mutation：T332N, A501C Mutation：T332N, A501C Mutation：I559P, T605C Mutation：I559P, T605C Mutation：I559P, T605C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.19 Å
9DMB Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer Deposited 2024-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain E 509–661（153 aa） Chain I 509–661（153 aa） Chain J 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.27 Å
9EHL Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOMAmin5 and 10-1074 Broadly Neutralizing Antibodies - Class I Deposited 2024-11-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 32–505（474 aa） Fragment：UNP residues 32-505 Chain B 32–505（474 aa） Fragment：UNP residues 32-505 Chain C 32–505（474 aa） Fragment：UNP residues 32-505 Chain D 509–661（153 aa） Fragment：UNP residues 509-661 Chain E 509–661（153 aa） Fragment：UNP residues 509-661 Chain F 509–661（153 aa） Fragment：UNP residues 509-661	Mutation：T326N,A494C Mutation：T326N,A494C Mutation：T326N,A494C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9EHM Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOMAmin5 and 10-1074 Broadly Neutralizing Antibodies - Class II Deposited 2024-11-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 32–505（474 aa） Fragment：UNP residues 32-505 Chain B 32–505（474 aa） Fragment：UNP residues 32-505 Chain C 32–505（474 aa） Fragment：UNP residues 32-505 Chain D 509–661（153 aa） Fragment：UNP residues 509-661 Chain E 509–661（153 aa） Fragment：UNP residues 509-661 Chain F 509–661（153 aa） Fragment：UNP residues 509-661	Mutation：T326N,A494C Mutation：T326N,A494C Mutation：T326N,A494C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9P6E N49P7-FR Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab Deposited 2025-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 18-meric	Chain A 30–510（481 aa） Chain C 30–510（481 aa） Chain E 30–510（481 aa）	Mutation：T105E, M270I, F287L, R303V, A316Y, T330N, N361Q, A498C, E506R, K507R, A509R, V510R Mutation：T105E, M270I, F287L, R303V, A316Y, T330N, N361Q, A498C, E506R, K507R, A509R, V510R Mutation：T105E, M270I, F287L, R303V, A316Y, T330N, N361Q, A498C, E506R, K507R, A509R, V510R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33	ELECTRON MICROSCOPY cryo-EM buffer pH 5.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9P6G eN49P7-FRv1-23 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab Deposited 2025-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 18-meric	Chain A 30–510（481 aa） Chain C 30–510（481 aa） Chain E 30–510（481 aa）	Mutation：T105E, M270I, F287L, R303V, A316Y, T330N, N361Q, A498C, E506R, K507R, A509R, V510R Mutation：T105E, M270I, F287L, R303V, A316Y, T330N, N361Q, A498C, E506R, K507R, A509R, V510R Mutation：T105E, M270I, F287L, R303V, A316Y, T330N, N361Q, A498C, E506R, K507R, A509R, V510R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36	ELECTRON MICROSCOPY cryo-EM buffer pH 5.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9PIT HIV-1 bnAb 1-23 in complex with BG505 MD39 SOSIP and RM19R Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 18-meric	Chain B 30–510（481 aa） Chain E 30–510（481 aa） Chain F 30–510（481 aa）	Mutation：T106E, M271I, F288L, R304V, A319Y, T332N, N363Q, A501C, E509R, K510R, A512R, V513R Mutation：T106E, M271I, F288L, R304V, A319Y, T332N, N363Q, A501C, E509R, K510R, A512R, V513R Mutation：T106E, M271I, F288L, R304V, A319Y, T332N, N363Q, A501C, E509R, K510R, A512R, V513R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9PIV HIV-1 bnAb 9-71 in complex with BG505 MD39 SOSIP and RM19R Deposited 2025-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 18-meric	Chain B 30–510（481 aa） Chain E 30–510（481 aa） Chain F 30–510（481 aa）	Mutation：T106E, M271I, F288L, R304V, A319Y, T332N, N363Q, A501C, E509R, K510R, A512R, V513R Mutation：T106E, M271I, F288L, R304V, A319Y, T332N, N363Q, A501C, E509R, K510R, A512R, V513R Mutation：T106E, M271I, F288L, R304V, A319Y, T332N, N363Q, A501C, E509R, K510R, A512R, V513R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9Q0W Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab Deposited 2025-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain B 509–661（153 aa） Chain D 509–661（153 aa） Chain F 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9Q3S Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664 Deposited 2025-08-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 30–508（479 aa） Chain B 509–661（153 aa） Chain C 509–661（153 aa） Chain G 30–508（479 aa） Chain I 30–508（479 aa） Chain J 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9Q3X The CryoEM structure of Rhesus macaque 1G3 and PGT121 Fabs in complex with BG505 SOSIP.664 Deposited 2025-08-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 30–508（479 aa） Chain B 509–661（153 aa） Chain C 509–661（153 aa） Chain G 30–508（479 aa） Chain I 30–508（479 aa） Chain J 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；phosphate buffered saline cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.64 Å
9Y9V THE CRYOEM STRUCTURE OF RHESUS MACAQUE 1A8 AND PGT121 FABS IN COMPLEX WITH BG505 SOSIP.664. Deposited 2025-09-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 30–508（479 aa） Chain B 509–661（153 aa） Chain C 509–661（153 aa） Chain G 30–508（479 aa） Chain I 30–508（479 aa） Chain J 509–661（153 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å

53 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q2N0S5_HV1
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–479； UniProt 30–508 Author chain G； PDBConstruct 1–479； UniProt 30–508 Author chain I； PDBConstruct 1–479； UniProt 30–508 Author chain B； PDBConstruct 1–153； UniProt 509–661 Author chain C； PDBConstruct 1–153； UniProt 509–661 Author chain J； PDBConstruct 1–153； UniProt 509–661

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9q09
Deposition date deposition_date	2025-08-12
Structure title title	Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab76 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664
Keywords keywords	HIV-1 Env, Broadly-neutralizing antibodies (bNAbs), glycan hole, CD4-binding site (CD4bs), VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	54.43 Å
Radius of gyration Rg (electron density) rg_electron	53.91 Å
Forward intensity I(0) i0	2185130000.00
Molecular weight molecular_weight	383500.0 kDa
Excluded volume excluded_volume	476600 Å³
Envelope volume envelope_volume	716090 Å³
Hydration-shell volume shell_volume	109170 Å³
Envelope diameter envelope_diameter	171.7 Å
Shell Rg shell_rg	58.40 Å
Envelope Rg envelope_rg	52.46 Å
Shape Rg shape_rg	53.94 Å
Total Rg total_rg	53.94 Å
Total atoms total_atoms	26904
Residues n_residues	3182
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

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

Maximum dimension Dmax dmax	170.1 Å
Rg (real space) rg_real	55.08 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	2.1450e+09
I(0) uncertainty (real space) i0_real_error	3.4520e+07
Rg (reciprocal space) rg_reciprocal	54.65 Å
I(0) (reciprocal space) i0_reciprocal	2187000000.0000
Solution quality estimate total_estimate	0.7227
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	70.4 Å
Skewness Skewness skewness	0.145
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	1.6030
Highest regularization parameter α highest_alpha	101600000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 0.923; Sysdev: 0.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.842

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (14)

Entity 1 Entity 1 polymer

Description description	BG505 SOSIP.664 gp120
Molecular weight formula_weight	54064.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,G,I
Atom count atom_count	26930

AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

来源 Source

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

Entity 2 Entity 2 polymer

Description description	BG505 SOSIP.664 gp41
Molecular weight formula_weight	17146.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,J

AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

来源 Source

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

Entity 3 Entity 3 polymer

Description description	Ab76 Fab heavy chain
Molecular weight formula_weight	24511.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,K

DVQLVESGGGLVKPGGSLRLSCVASGFSFSSYEMHWVRQAPGKGLEWVSYFSDTGGITYYADSVKGRFTISRDNAENSLFLQMNNLRVEDTAVYYCARGGYTGSWIDLFDLWGQGVLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGGSK

来源 Source

来源生物 organism	Macaca mulatta
NCBI Class编号 ncbi_taxonomy_id	9544
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Ab76 Fab light chain
Molecular weight formula_weight	23473.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,L,M

KAILTQPASLSASPGASASLTCTFSGGIHVAGYHIFWYQQKPGSPPRYLLRYKSDSDKAQGSGVPSRFSGSKDASANTGILRISGLQSEDEADYYCAIGHSDGHGLFGGGTRLTVLGQPKASPLVTLFPPSSEELQANKATLVCLISDFYPGVVKVAWKADGNSVNTGVETTTPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Macaca mulatta
NCBI Class编号 ncbi_taxonomy_id	9544
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	PGT121 Fab heavy chain
Molecular weight formula_weight	25169.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	h,d,k

QMQLQESGPGLVKPSETLSLTCSVSGASISDSYWSWIRRSPGKGLEWIGYVHKSGDTNYSPSLKSRVNLSLDTSKNQVSLSLVAATAADSGKYYCARTLHGRRIYGIVAFNEWFTYFYMDVWGNGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	PGT121 Fab light chain
Molecular weight formula_weight	22869.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	l,e,m

QVQIDISVAPGETARISCGEKSLGSRAVQWYQHRAGQAPSLIIYNNQDRPSGIPERFSGSPDSPFGTTATLTITSVEAGDEADYYCHIWDSRVPTKWVFGGGTTLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 7 Entity 7 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	26

Entity 8 Entity 8 branched

Description description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	6

Entity 9 Entity 9 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	4

Entity 10 Entity 10 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1559.4 kDa
Source method src_method	man
Copy count entity_count	3

Entity 11 Entity 11 branched

Description description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	3

Entity 12 Entity 12 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 13 Entity 13 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	17

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.23 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	332541

fit	/app/data/saxs_computation/q0/9q09/9q09.fit
pddf	/app/data/pr_computation/q0/9q09/9q09.pr.out
profile	/app/data/saxs_computation/q0/9q09/9q09.dat

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab76 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664

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

BG505 SOSIP.664 gp120

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (14)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 branched

Entity 10 Entity 10 branched

Entity 11 Entity 11 branched

Entity 12 Entity 12 branched

Entity 13 Entity 13 branched

Entity 14 Entity 14 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)