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6w03

Crystal Structure of HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.3 Angstrom

Method: X-RAY DIFFRACTION Dmax: 182.1 Å Quality: SUSPICIOUS
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp41

Human immunodeficiency virus 1

UniProt Q2N0S6

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 30 PDB declaration: octadecameric（18） Consistent with protein copy count Chain B； UniProt 509–661 Chain G； UniProt 30–504 Fragment：ectodomain Mutation：I559P, T605C Mutation：N137A, I201C, N302M, T320L, A329P, T332N, A433C, A501C 35O22 scFv heavy chain × 3 35O22 scFv light chain × 3 3H109L Fab heavy chain × 3 3H109L Fab light chain × 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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ;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 ; × 3 ;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-(1-3)-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-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 ; × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；298 K；75 mM imidazole pH6.5, 150 mM LiSO4, 3.8% PEG MPD and 6.2% PEG 3,350 Resolution 2.40 Å R-free 0.273

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 6W03 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3J5M Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs Deposited 2013-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 30–504（475 aa） Fragment：UNP residues 30-504
Chain E 30–504（475 aa） Fragment：UNP residues 30-504
Chain I 30–504（475 aa） Fragment：UNP residues 30-504
Mutation：T332N,A501C Mutation：T332N,A501C Mutation：T332N,A501C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer TBS；pH 7.5；TBS
cryo-EM vitrification conditions Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 seconds, followed by blotting with a small piece of filter paper and plunge-freezing into liquid ethane using a manual cryo-plunger in an ambient environment (4 C).；Cryogen ETHANE；3 uL sample applied to grid, adsorbed for 30 seconds, blotted, and plunge-frozen in liquid ethane
Resolution 5.80 Å
4NCO Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122 Deposited 2013-10-24 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 30–504（475 aa） Fragment：UNP residues 30-504
Chain E 30–504（475 aa） Fragment：UNP residues 30-504
Chain I 30–504（475 aa） Fragment：UNP residues 30-504
Mutation：T332N,A501C Mutation：T332N,A501C Mutation：T332N,A501C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；0.1 M CAPS, 2 M ammonium sulfate, 0.2 M lithium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 4.70 Å R-free 0.389
4ZMJ Crystal Structure of Ligand-Free BG505 SOSIP.664 HIV-1 Env Trimer Deposited 2015-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain B 509–661（153 aa）
Chain G 30–504（475 aa）
Mutation：I559P, T605C Mutation：T332N, A501C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；26% PEG 400, 3.2% PEG 3350, and 0.1M sodium acetate pH 5.5
Resolution 3.31 Å R-free 0.285
5ACO Cryo-EM structure of PGT128 Fab in complex with BG505 SOSIP.664 Env trimer Deposited 2015-08-17 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 × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa） Fragment：GP120, RESIDUES 30-505
Chain B 509–661（153 aa） Fragment：GP41, RESIDUES 509-661
Chain C 30–505（476 aa） Fragment：GP120, RESIDUES 30-505
Chain D 30–505（476 aa） Fragment：GP120, RESIDUES 30-505
Chain E 509–661（153 aa） Fragment：GP41, RESIDUES 509-661
Chain F 509–661（153 aa） Fragment：GP41, RESIDUES 509-661
Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer 50 MM TRIS, 150 MM NACL, 0.675 MM DDM；pH 7.4；50 MM TRIS, 150 MM NACL, 0.675 MM DDM
cryo-EM vitrification conditions Cryogen ETHANE；FROZEN IN LIQUID ETHANE AT 4 DEGREES C.
Resolution 4.36 Å
5C7K Crystal structure BG505 SOSIP gp140 HIV-1 Env trimer bound to broadly neutralizing antibodies PGT128 and 8ANC195 Deposited 2015-06-24 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 C 30–507（478 aa） Fragment：UNP Residues 30-507
Chain D 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；280 K；0.05 M lithium sulfate, 0.05 M sodium sulfate, 26% (w/v) PEG 400 and 0.1 M Tris-HCl pH 8.3
Resolution 4.60 Å R-free 0.295
5CEZ Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with an early putative precursor of the PGT121 family at 3.0 Angstrom Deposited 2015-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 31–508（478 aa） Fragment：UNP residues 31-505
Mutation：N137A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MAN alpha-D-mannopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2 M CaCl2, 28% (v/v) PEG 400 and 0.1 M Hepes pH 7.5
Resolution 3.03 Å R-free 0.266
5CEZ Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with an early putative precursor of the PGT121 family at 3.0 Angstrom Deposited 2015-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MAN alpha-D-mannopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2 M CaCl2, 28% (v/v) PEG 400 and 0.1 M Hepes pH 7.5
Resolution 3.03 Å R-free 0.266
5CJX Crystal structure of 8ANC195 Fab in complex with BG505 SOSIP.664 HIV-1 Env trimer Deposited 2015-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 32–505（474 aa） Fragment：UNP residues 32-505
Chain J 509–661（153 aa） Fragment：UNP residues 509-661
Chain K 32–505（474 aa） Fragment：UNP residues 32-505
Chain X 509–661（153 aa） Fragment：UNP residues 509-661
Chain Y 32–505（474 aa） Fragment：UNP residues 32-505
Mutation：I559P, T605C Mutation：T332N, A501C Mutation：I559P, T605C Mutation：T332N, A501C Mutation：I559P, T605C Mutation：T332N, A501C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；0.1 M Tris, pH 8.0, 15% PEG3350, 2% v/v 1,4-dioxane
Resolution 3.58 Å R-free 0.286
5D9Q Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122 and scFv NIH45-46 Deposited 2015-08-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain A 30–501（472 aa）
Chain G 30–501（472 aa）
Chain J 30–501（472 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.4 M ammonium sulfate, 0.1 M Tris, pH 8.0
Resolution 4.40 Å R-free 0.320
5FYL Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122 and 35O22 Deposited 2016-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 509–661（153 aa） Fragment：GP120 ENV ECTODOMAIN
Chain G 30–505（476 aa） Fragment：GP120 ENV ECTODOMAIN
Mutation：YES Mutation：YES NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.18 M LI2SO4, 4.79% PEG 1500, 14.4% ISOPROPANOL, 10 MM YTTRIUM CHLORIDE, 0.09 M SODIUM ACETATE PH 5.5
Resolution 3.10 Å R-free 0.307
5I8H Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3 Loop-targeting Antibody PGT122 Fab and Fusion Peptide-targeting Antibody VRC34.01 Fab Deposited 2016-02-18 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: octadecameric
Chain A 30–508（479 aa）
Chain B 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.5M Sodium Chloride, 0.1M Tris-HCl pH8.5, 5% PEG 8000 and 20% 2-methyl-2, 4- pentanediol
Resolution 4.30 Å R-free 0.309
5I8H Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3 Loop-targeting Antibody PGT122 Fab and Fusion Peptide-targeting Antibody VRC34.01 Fab Deposited 2016-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain C 30–508（479 aa）
Chain D 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.5M Sodium Chloride, 0.1M Tris-HCl pH8.5, 5% PEG 8000 and 20% 2-methyl-2, 4- pentanediol
Resolution 4.30 Å R-free 0.309
5T3S HIV gp140 trimer MD39-10MUTA in complex with Fabs PGT124 and 35022 Deposited 2016-08-26 Different construct Different mutation/modification 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 G 30–505（476 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.1；277 K；5% Peg6000 0.1M citric acid
Resolution 4.50 Å R-free 0.309
5T3X 3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074. Deposited 2016-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-611
Chain G 30–508（479 aa） Fragment：UNP residues 30-508
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM ammonium citrate tribasic pH 7.0 100 mM imidazole pH 7.0 20% PEG MME 2,000
Resolution 3.90 Å R-free 0.331
5T3Z 3.5 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074 Deposited 2016-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-611
Chain G 30–508（479 aa） Fragment：UNP residues 30-508
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM ammonium citrate tribasic pH 7.0 100 mM imidazole pH 7.0 20% PEG MME 2,000
Resolution 3.50 Å R-free 0.306
5THR Cryo-EM structure of a BG505 Env-sCD4-17b-8ANC195 complex Deposited 2016-09-30 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 × 21 PDB declaration: 21-meric
Chain A 509–661（153 aa） Fragment：UNP residues 509-661
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 509–661（153 aa） Fragment：UNP residues 509-661
Chain D 30–505（476 aa） Fragment：UNP residue 30-505
Chain E 30–505（476 aa） Fragment：UNP residue 30-505
Chain F 30–505（476 aa） Fragment：UNP residue 30-505
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.90 Å
5U1F Initial contact of HIV-1 Env with CD4: Cryo-EM structure of BG505 DS-SOSIP trimer in complex with CD4 and antibody PGT145 Deposited 2016-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 29–502（474 aa） Fragment：UNP residues 29-502
Chain B 508–661（154 aa）
Chain C 29–502（474 aa） Fragment：UNP residues 29-502
Chain D 29–502（474 aa） Fragment：UNP residues 29-502
Chain E 508–661（154 aa）
Chain F 508–661（154 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
5UTF Crystal Structure of a Stabilized DS-SOSIP.6mut BG505 gp140 HIV-1 Env Trimer, Containing Mutations I201C-P433C (DS), L154M, Y177W, N300M, N302M, T320L, I420M in Complex with Human Antibodies PGT122 and 35O22 at 4.3 A Deposited 2017-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 509–661（153 aa）
Chain G 30–510（481 aa）
Mutation：I201C-P433C (DS) Mutation：L154M, Y177W, N300M, N302M, T320L, I420M NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；13.2% PEG 400, 6.6% PEG 8000, 0.1M. Sodium acetate/Acetic acid pH 4.5
Resolution 3.50 Å R-free 0.299
5UTY Crystal Structure of a Stabilized DS-SOSIP.mut4 BG505 gp140 HIV-1 Env Trimer, Containing Mutations I201C-P433C (DS), L154M, N300M, N302M, T320L in Complex with Human Antibodies PGT122 and 35O22 at 4.1 Angstrom Deposited 2017-02-15 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） Fragment：UNP residues 509-661
Chain G 29–505（477 aa） Fragment：UNP residues 29-505
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；10.5% PEG 4000, 0.2M AmSO4, 0.1M NaoAc pH 4.6
Resolution 3.41 Å R-free 0.288
5V7J Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Four Glycans (N197, N276, N362, and N462) removed in Complex with Neutralizing Antibodies 3H+109L and 35O22. Deposited 2017-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 31–505（475 aa） Fragment：UNP residues 31-505
Mutation：S198A, T278A, S365A, T464A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；4.95% isopropanol, 8.25% PEG 3350, 0.2M ammonium citrate, pH 4.5
Resolution 2.91 Å R-free 0.339
5V8L BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies 3BNC117 and PGT145 Deposited 2017-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–505（476 aa） Fragment：UNP residues 30-505
Chain D 30–505（476 aa） Fragment：UNP residues 30-505
Chain E 509–661（153 aa） Fragment：UNP residues 509-661
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
5V8M BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibody 3BNC117 Deposited 2017-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain F 30–505（476 aa） Fragment：UNP residues 30-505
Chain G 30–505（476 aa） Fragment：UNP residues 30-505
Chain I 509–661（153 aa） Fragment：UNP residues 509-661
Chain J 509–661（153 aa） Fragment：UNP residues 509-661
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 4.40 Å
5VIY BG505 SOSIP.664 in complex with broadly neutralizing antibodies BG1 and 8ANC195 Deposited 2017-04-17 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 × 16 PDB declaration: hexadecameric
Chain A 509–661（153 aa） Fragment：UNP residues 509-661
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 509–661（153 aa） Fragment：UNP residues 509-661
Chain D 30–508（479 aa） Fragment：UNP residues 30-505
Chain E 30–508（479 aa） Fragment：UNP residues 30-505
Chain F 30–508（479 aa） Fragment：UNP residues 30-505
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 6.20 Å
5VJ6 BG505 SOSIP.664 in complex with broadly neutralizing antibodies PG9 and 8ANC195 Deposited 2017-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 509–661（153 aa） Fragment：UNP residues 509-661
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 509–661（153 aa） Fragment：UNP residues 509-661
Chain D 30–505（476 aa） Fragment：UNP residues 30-505
Chain E 30–505（476 aa） Fragment：UNP residues 30-505
Chain F 30–505（476 aa） Fragment：UNP residues 30-505
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 11.50 Å
5W6D Crystal structure of BG505-SOSIP.v4.1-GT1-N137A in complex with Fabs 35022 and 9H/109L Deposited 2017-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；0.2M NaCl, 34% PEG 300, 0.1M NaOAc
Resolution 3.20 Å R-free 0.267
5WDU HIV-1 Env BG505 SOSIP.664 H72C-H564C trimer in complex with bNAbs PGT122 Fab, 35O22 Fab and NIH45-46 scFv Deposited 2017-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 21-meric
Chain F 31–501（471 aa）
Chain G 31–501（471 aa）
Chain Q 31–501（471 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8% (w/v) polyethylene glycol 8000, 0.1 M Tris, pH 8.5
Resolution 7.00 Å R-free 0.363
6B0N Crystal structure of the cleavage-independent prefusion HIV Env glycoprotein trimer of the clade A BG505 isolate (NFL construct) in complex with Fabs PGT122 and PGV19 at 3.39 A Deposited 2017-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain G 30–503（474 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 MAN alpha-D-mannopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1M HEPES (pH 7.0), 15% (w/v) PEG4000, and cryo-protected with 25% glycerol
Resolution 3.40 Å R-free 0.346
6CH7 XFEL crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22 Deposited 2018-02-22 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 G 30–508（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；5% Tacismate pH 8.0, 14% PEG 3350, 0.1M Tris pH 8.0
Resolution 3.80 Å R-free 0.262
6CH8 Crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22 Deposited 2018-02-22 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 G 30–508（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；5% Tacismate pH 8.0, 15% PEG 3350
Resolution 4.10 Å R-free 0.274
6CHB Crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and IOMA Deposited 2018-02-22 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 F 30–508（479 aa）
Chain G 30–508（479 aa）
Chain H 30–508（479 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；5% Tacismate pH 8.0, 15% PEG 3350
Resolution 6.80 Å R-free 0.417
6CUE Cryo-EM structure at 4.0 A resolution of vaccine-elicited antibody vFP7.04 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122 Deposited 2018-03-26 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 × 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 × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6CUF Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody vFP1.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122 Deposited 2018-03-26 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 × 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 × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6DE7 Crystal Structure at 4.3 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Interdomain Stabilization 113C-429GCG in Complex with Broadly Neutralizing Antibodies PGT122 and 35O22 Deposited 2018-05-11 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: octadecameric
Chain G 30–510（481 aa）
Mutation：D113C, T332N, R429G, A501C, E509R, K510R, A512R, V513R NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；24%PEG400, 3% PEG3350, 0.1M sodium acetate 5.5, 0.2M LiSO4
Resolution 4.12 Å R-free 0.258
6DFG BG505 MD39 SOSIP trimer in complex with mature BG18 fragment antigen binding Deposited 2018-05-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa）
Chain C 30–505（476 aa）
Chain D 30–505（476 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；3.5 second blot time
Resolution 4.42 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa）
Chain C 30–505（476 aa）
Chain D 30–505（476 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
6DID HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1 Deposited 2018-05-23 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 × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa） Fragment：GP120 domain residues 30-505
Chain F 30–505（476 aa） Fragment：GP120 domain residues 30-505
Chain G 30–505（476 aa） Fragment：GP120 domain residues 30-505
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 4.71 Å
6E5P Backbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03 Deposited 2018-07-21 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 × 24 PDB declaration: 24-meric
Chain A 30–503（474 aa）
Chain C 30–503（474 aa）
Chain E 30–503（474 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.01
cryo-EM vitrification conditions Cryogen ETHANE；0.005% dodecyl maltoside was added to sample before vitification
Resolution 8.80 Å
6MAR HIV-1 Envelope Glycoprotein Clone BG505 delCT N332T in complex with broadly neutralizing antibody Fab PGT151 Deposited 2018-08-28 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 × 10 PDB declaration: decameric
Chain A 30–502（473 aa）
Chain C 30–502（473 aa）
Chain E 30–502（473 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6MN7 Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding fragment Deposited 2018-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 30–505（476 aa）
Chain C 30–505（476 aa）
Chain D 30–505（476 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6MPG Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody, A12V163-b.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122 Deposited 2018-10-06 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 × 24 PDB declaration: 24-meric
Chain 2 30–502（473 aa）
Chain C 30–502（473 aa）
Chain V 30–502（473 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
Resolution 3.20 Å
6MPH Cryo-EM structure at 3.8 A resolution of HIV-1 fusion peptide-directed antibody, DF1W-a.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122 Deposited 2018-10-06 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 × 24 PDB declaration: 24-meric
Chain A 30–502（473 aa）
Chain B 30–502（473 aa）
Chain C 30–502（473 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6MTJ 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 3H109L and 35O22 at 2.9 Angstrom Deposited 2018-10-19 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: octadecameric
Chain B 509–661（153 aa） Fragment：gp41
Chain G 30–505（476 aa） Fragment：gp120
Mutation：I559P, A605C Mutation：N137A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 83G 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；75mM Imidazole pH6.5 3.75% MPD 6.25% PEG 3,350 150mM LiSO4
Resolution 2.34 Å R-free 0.281
6MTN Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor Compound 484 in Complex with Human Antibodies 3H109L and 35O22 at 3.0 Angstrom Deposited 2018-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 509–661（153 aa） Fragment：gp41
Chain G 30–505（476 aa） Fragment：gp120
Mutation：I559P, A605C Mutation：N137A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 JYJ {4-[1-(3-chlorophenyl)cyclopropane-1-carbonyl]piperazin-1-yl}(thiophen-3-yl)methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；60mM Imidazole pH6.5 3% MPD 5% PEG3,350 120mM LiSO$
Resolution 2.50 Å R-free 0.263
6MU6 Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-814508 in Complex with Human Antibodies 3H109L and 35O22 at 3.2 Angstrom Deposited 2018-10-22 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） Fragment：gp41
Chain G 30–505（476 aa） Fragment：gp120
Mutation：I559P, A605C Mutation：N137A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 JYV (2R)-{1-[{7-[2-({[3-(dimethylamino)propyl](methyl)amino}methyl)-1,3-thiazol-4-yl]-4-methoxy-1H-pyrrolo[2,3-c]pyridin-3-yl}(oxo)acetyl]piperidin-4-yl}(phenyl)acetonitrile × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；60mM imidazole pH6.5 3% MPD 5% PEG3,350 120mM LiSO4
Resolution 2.55 Å R-free 0.264
6MU7 Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-818251 in Complex with Human Antibodies 3H109L and 35O22 at 3.1 Angstrom Deposited 2018-10-22 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） Fragment：gp41
Chain G 30–505（476 aa） Fragment：gp120
Mutation：I559P, A605C Mutation：N137A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 JYY 4-{3-[{4-[(R)-cyano(phenyl)methyl]piperidin-1-yl}(oxo)acetyl]-4-methoxy-1H-pyrrolo[2,3-c]pyridin-7-yl}-N-(2-hydroxyethyl)-1,3-thiazole-2-carboxamide × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；150mM Ammonium Citrate pH7.5 7.5% PEG3,350 7.5% isopropanol
Resolution 2.50 Å R-free 0.261
6MU8 Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-386150 in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom Deposited 2018-10-22 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） Fragment：gp41
Chain G 30–505（476 aa） Fragment：gp120
Mutation：I559P, A605C Mutation：N137A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 JYS 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-1,2-dione × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；60mM imidazole pH6.5 3% MPD 5% PEG3,350 120mM LiSO4
Resolution 2.99 Å R-free 0.259
6N1V Cryo-EM structure at 4.0 A resolution of vaccine-elicited antibody A12V163-a.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122 Deposited 2018-11-12 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 × 24 PDB declaration: 24-meric
Chain A 30–502（473 aa）
Chain B 30–502（473 aa）
Chain C 30–502（473 aa）
Chain D 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 × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6N1W Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody DFPH-a.15 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122 Deposited 2018-11-12 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 × 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 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6NF2 Cryo-EM structure of vaccine-elicited antibody 0PV-c.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122 Deposited 2018-12-18 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 × 24 PDB declaration: 24-meric
Chain A 30–509（480 aa）
Chain B 509–661（153 aa）
Chain G 30–509（480 aa）
Chain I 509–661（153 aa）
Chain Q 30–509（480 aa）
Chain R 509–661（153 aa）
Mutation：I201C, T332N, A433C, A501C, E509R, K510R, A512R Mutation：I559P, T605C Mutation：I201C, T332N, A433C, A501C, E509R, K510R, A512R Mutation：I559P, T605C Mutation：I201C, T332N, A433C, A501C, E509R, K510R, A512R Mutation：I559P, T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6NM6 Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to N6 FR3-03 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.2 Angstrom Deposited 2019-01-10 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 B 509–661（153 aa） Fragment：Ectodomain
Chain G 30–505（476 aa）
Mutation：I559P, T605C Mutation：N137A, T332N, A501C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；60 mM acetate pH 4.5, 420 mM sodium formate, 5% PEG 3,350 and 60 mM CaCl2
Resolution 2.74 Å R-free 0.288
6NNF Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to VRC01 FR3-03 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.5 Angstrom Deposited 2019-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 24-meric
Chain B 509–661（153 aa） Fragment：gp41
Chain G 30–505（476 aa） Fragment：gp120
Mutation：I559P, A605C Mutation：N137A, T332N, A501C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；72 mM imidazole pH 6.5, 72 mM
Resolution 2.76 Å R-free 0.298
6NNJ Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.1 Angstrom Deposited 2019-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 24-meric
Chain B 509–661（153 aa） Fragment：gp41
Chain G 30–505（476 aa） Fragment：gp120
Mutation：I559P, A605C Mutation：N137A, T332N, A501C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；298 K；90 mM imidazole pH 6.5, 90 mM MgCl2, 0.6 M NaCl and 6% PEG 3,350
Resolution 2.60 Å R-free 0.293
6OPA Crystal structure of bovine Fab NC-Cow1 in complex with HIV-1 BG505 SOSIP.664, and human Fabs 35022 and PGT128 Deposited 2019-04-24 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 B 509–661（153 aa）
Chain G 30–504（475 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.56；298 K；0.2M sodium citrate, 0.1M Tris, 30% Peg400
Resolution 4.08 Å R-free 0.343
6OSY Cryo-EM structure of vaccine-elicited antibody 0PV-a.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122 Deposited 2019-05-02 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 × 24 PDB declaration: 24-meric
Chain 2 30–508（479 aa）
Chain B 30–508（479 aa）
Chain K 30–508（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6OT1 Cryo-EM structure of vaccine-elicited antibody 0PV-b.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122 Deposited 2019-05-02 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 × 24 PDB declaration: 24-meric
Chain B 509–661（153 aa）
Chain D 509–661（153 aa）
Chain E 30–508（479 aa）
Chain G 30–508（479 aa）
Chain O 509–661（153 aa）
Chain P 30–508（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OZ4 Crystal structure of broadly neutralizing antibody N49P6 Fab in complex with HIV-1 BG505 SOSIP.664 Env trimer ectodomain. Deposited 2019-05-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 509–661（153 aa）
Chain G 30–505（476 aa）
Mutation：I559P, T605C Mutation：T330N, A498C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；12% PEG 3350 0.1 M Tris-HCl pH 8.0
Resolution 4.05 Å R-free 0.315
6OZC BG505 SOSIP.664 with 2G12 Fab2 Deposited 2019-05-15 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 30–504（475 aa）
Chain B 509–661（153 aa）
Chain E 30–504（475 aa）
Chain F 30–504（475 aa）
Chain G 509–661（153 aa）
Chain I 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 3.79 Å
6PW6 The HIV-1 Envelope Glycoprotein Clone BG505 SOSIP.664 in Complex with Three Copies of the Bovine Broadly Neutralizing Antibody, NC-Cow1, Fragment Antigen Binding Domain Deposited 2019-07-22 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 × 9 PDB declaration: nonameric
Chain A 30–505（476 aa）
Chain B 509–661（153 aa）
Chain C 30–505（476 aa）
Chain D 509–661（153 aa）
Chain E 30–505（476 aa）
Chain F 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6U0L Asymmetrically open conformational state (Class I) of HIV-1 Env trimer BG505 SOSIP.664 in complex with sCD4 and E51 Fab Deposited 2019-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain A 30–505（476 aa）
Chain B 30–505（476 aa）
Chain C 30–505（476 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 × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6U0N Asymmetrically open conformational state (Class II) of HIV-1 Env trimer BG505 SOSIP.664 in complex with sCD4 and E51 Fab Deposited 2019-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain A 32–505（474 aa）
Chain B 32–505（474 aa）
Chain C 32–505（474 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 × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6UDJ HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074 Deposited 2019-09-19 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 C 509–661（153 aa） Fragment：UNP residues 509-661
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 32–505（474 aa） Fragment：UNP residues 32-505
Chain J 32–505（474 aa） Fragment：UNP residues 32-505
Chain M 509–661（153 aa） Fragment：UNP residues 509-661
Chain P 32–505（474 aa） Fragment：UNP residues 32-505
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；0 blot force, 3.0 second blot time, 3 uL sample added to freshly glow discharged grids
Resolution 2.50 Å
6UTK Crystal structure of 438-B11 Fab in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22 at 3.80 Angstrom Deposited 2019-10-29 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 G 30–503（474 aa） Fragment：UNP residues 30-503
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M sodium chloride, 36% v/v PEG400, 0.1 M sodium/potassium phosphate, pH 5.7
Resolution 3.80 Å R-free 0.317
6V0R BG505 SOSIP.664 Trimer Deposited 2019-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 30–504（475 aa） Fragment：UNP residues 30-504
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–504（475 aa） Fragment：UNP residues 30-504
Chain D 30–504（475 aa） Fragment：UNP residues 30-504
Chain E 509–661（153 aa） Fragment：UNP residues 509-661
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
6V6W Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22 Deposited 2019-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain G 30–503（474 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；12% 1-propanol, 0.1M MES (pH=6.5), 20% polyethylene glycol monomethyl ether 5000, 25% glycerol
Resolution 6.50 Å R-free 0.355
6V6W Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22 Deposited 2019-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain C 30–503（474 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；12% 1-propanol, 0.1M MES (pH=6.5), 20% polyethylene glycol monomethyl ether 5000, 25% glycerol
Resolution 6.50 Å R-free 0.355
6V8X VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure Deposited 2019-12-12 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 × 12 PDB declaration: dodecameric
Chain A 32–502（471 aa） Fragment：UNP residues 32-502
Chain E 32–502（471 aa） Fragment：UNP residues 32-502
Chain I 32–502（471 aa） Fragment：UNP residues 32-502
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6V8Z VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure Deposited 2019-12-12 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 × 18 PDB declaration: octadecameric
Chain A 31–502（472 aa） Fragment：UNP residues 31-502
Chain G 31–502（472 aa） Fragment：UNP residues 31-502
Chain M 31–502（472 aa） Fragment：UNP residues 31-502
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 2.90 Å
6VI0 Cryo-EM structure of VRC01.23 in complex with HIV-1 Env BG505 DS.SOSIP Deposited 2020-01-10 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 × 12 PDB declaration: dodecameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 30–508（479 aa）
Chain F 509–661（153 aa）
Chain G 30–508（479 aa）
Chain I 30–508（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
6VKN BG505 SOSIP.v5.2.N241.N289 in complex with rhesus macaque Fab RM19R Deposited 2020-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 30–504（475 aa）
Chain B 509–661（153 aa）
Chain C 30–504（475 aa）
Chain D 30–504（475 aa）
Chain E 509–661（153 aa）
Chain F 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6VLR BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab Deposited 2020-01-24 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 × 14 PDB declaration: tetradecameric
Chain A 30–504（475 aa）
Chain B 509–661（153 aa）
Chain G 30–504（475 aa）
Chain H 30–504（475 aa）
Chain I 509–661（153 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
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.42 Å
6VN0 BG505 SOSIP.v4.1 in complex with rhesus macaque Fab RM20F Deposited 2020-01-29 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 × 12 PDB declaration: dodecameric
Chain A 30–504（475 aa）
Chain B 509–661（153 aa）
Chain C 30–504（475 aa）
Chain D 30–504（475 aa）
Chain E 509–661（153 aa）
Chain F 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 4.25 Å
6VO0 BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2 Deposited 2020-01-29 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 × 12 PDB declaration: dodecameric
Chain A 30–504（475 aa）
Chain B 509–661（153 aa）
Chain C 30–504（475 aa）
Chain D 30–504（475 aa）
Chain E 509–661（153 aa）
Chain F 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
6VO1 BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20J Deposited 2020-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 30–504（475 aa）
Chain B 509–661（153 aa）
Chain C 30–504（475 aa）
Chain D 30–504（475 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
Resolution 3.88 Å
6X96 Cryo-EM model of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 10A fragment antigen binding variable domain Deposited 2020-06-02 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 × 12 PDB declaration: dodecameric
Chain A 30–510（481 aa）
Chain B 509–661（153 aa）
Chain C 30–510（481 aa）
Chain D 509–661（153 aa）
Chain G 30–510（481 aa）
Chain I 509–661（153 aa）
Mutation：T332N, A501C, E509R, K510R, A512R, V513R Mutation：I559P, T605C Mutation：T332N, A501C, E509R, K510R, A512R, V513R Mutation：I559P, T605C Mutation：T332N, A501C, E509R, K510R, A512R, V513R Mutation：I559P, T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent (DDM) added shortly prior to freezing
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6X97 Cryo-EM model of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11A fragment antigen binding variable domain Deposited 2020-06-02 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 × 12 PDB declaration: dodecameric
Chain A 30–510（481 aa）
Chain B 509–661（153 aa）
Chain C 30–510（481 aa）
Chain D 509–661（153 aa）
Chain G 30–510（481 aa）
Chain I 509–661（153 aa）
Mutation：T332N, A501C, E509R, K510R, A512R, V513R Mutation：I559P, T605C Mutation：T332N, A501C, E509R, K510R, A512R, V513R Mutation：I559P, T605C Mutation：T332N, A501C, E509R, K510R, A512R, V513R Mutation：I559P, T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent (DDM) added shortly prior to freezing
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.65 Å
6X98 Cryo-EM model of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding variable domain Deposited 2020-06-02 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 × 12 PDB declaration: dodecameric
Chain A 30–510（481 aa）
Chain B 509–661（153 aa）
Chain C 30–510（481 aa）
Chain D 509–661（153 aa）
Chain G 30–510（481 aa）
Chain I 509–661（153 aa）
Mutation：T332N, A501C, E509R, K510R, A512R, V513R Mutation：I559P, T605C Mutation：T332N, A501C, E509R, K510R, A512R, V513R Mutation：I559P, T605C Mutation：T332N, A501C, E509R, K510R, A512R, V513R Mutation：I559P, T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent (DDM) added shortly prior to freezing
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
6X9R HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in HEK293F cells in complex with RM20A3 Fab Deposited 2020-06-03 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 × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6X9R HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in HEK293F cells in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6X9R HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in HEK293F cells in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6X9S HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in stable CHO cells in complex with RM20A3 Fab Deposited 2020-06-03 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 × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6X9S HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in stable CHO cells in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6X9S HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in stable CHO cells in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6X9T HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in HEK293S cells in complex with RM20A3 Fab Deposited 2020-06-03 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 × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6X9T HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in HEK293S cells in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6X9T HIV-1 Envelope Glycoprotein BG505 SOSIP.664 expressed in HEK293S cells in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6X9U HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and partially deglycosylated by endoglycosidase H, in complex with RM20A3 Fab Deposited 2020-06-03 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 × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6X9U HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and partially deglycosylated by endoglycosidase H, in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6X9U HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and partially deglycosylated by endoglycosidase H, in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6X9V HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and deglycosylated by endoglycosidase H, in complex with RM20A3 Fab Deposited 2020-06-03 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 × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6X9V HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and deglycosylated by endoglycosidase H, in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6X9V HIV-1 Envelope Glycoprotein BG505 SOSIP.664, expressed in HEK293S cells and deglycosylated by endoglycosidase H, in complex with RM20A3 Fab Deposited 2020-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa）
Mutation：T332N,A501C Mutation：I559P,T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6XRT Cryo-EM structure of SHIV-elicited RHA1.V2.01 in complex with HIV-1 Env BG505 DS-SOSIP.664 Deposited 2020-07-13 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 × 8 PDB declaration: octameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 30–505（476 aa）
Chain F 30–505（476 aa）
Chain G 30–505（476 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 40 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7KDE BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485 and human gp120-gp41 interface antibody 8ANC195 Deposited 2020-10-08 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 A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–505（474 aa）
Chain F 32–505（474 aa）
Chain G 32–505（474 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；3s blot, blot force 0
Resolution 3.55 Å
7LG6 BG505 SOSIP.v5.2 in complex with VRC40.01 and RM19R Fabs Deposited 2021-01-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 30–504（475 aa）
Chain B 509–661（153 aa）
Chain E 30–504（475 aa）
Chain F 30–504（475 aa）
Chain G 509–661（153 aa）
Chain I 509–661（153 aa）
Mutation：E64K, A73C, A316W, T332N, A501C Mutation：I559P, A561C, T605C Mutation：E64K, A73C, A316W, T332N, A501C Mutation：E64K, A73C, A316W, T332N, A501C Mutation：I559P, A561C, T605C Mutation：I559P, A561C, T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7LL1 Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly neutralizing antibody VRC40.01 Fab Deposited 2021-02-03 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 × 12 PDB declaration: dodecameric
Chain A 30–502（473 aa）
Chain C 30–502（473 aa）
Chain G 30–502（473 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2.5 S before plunging
Resolution 3.73 Å
7LL2 Cryo-EM structure of BG505 DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody VRC33.01 Fab Deposited 2021-02-03 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 × 12 PDB declaration: dodecameric
Chain A 30–502（473 aa）
Chain C 30–502（473 aa）
Chain E 30–502（473 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 3.73 Å
7LO6 Structure of CD4 mimetic BNM-III-170 in complex with BG505 SOSIP.664 HIV-1 Env trimer and 17b Fab Deposited 2021-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 32–508（477 aa）
Chain B 509–661（153 aa）
Chain C 32–508（477 aa）
Chain D 509–661（153 aa）
Chain E 32–508（477 aa）
Chain F 509–661（153 aa）
Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 5VG ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7LOK Structure of CD4 mimetic M48U1 in complex with BG505 SOSIP.664 HIV-1 Env trimer and 17b Fab Deposited 2021-02-10 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 × 13 PDB declaration: tridecameric
Chain A 32–508（477 aa）
Chain B 509–661（153 aa）
Chain C 32–508（477 aa）
Chain D 509–661（153 aa）
Chain E 32–508（477 aa）
Chain F 509–661（153 aa）
Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 Mutation：BG505 SOSIP.664 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7LPN Cryo-EM structure of llama J3 VHH antibody in complex with HIV-1 Env BG505 DS-SOSIP.664 Deposited 2021-02-12 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 × 9 PDB declaration: nonameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 30–505（476 aa）
Chain E 509–661（153 aa）
Chain F 30–505（476 aa）
Chain G 30–505（476 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.61 Å
7MDT BG505 SOSIP.v5.2 in complex with the monoclonal antibody Rh4O9.8 (as Fab fragment) Deposited 2021-04-06 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 × 8 PDB declaration: octameric
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）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；TBS, 0.2um filtered
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7MDU BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3 Deposited 2021-04-06 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 A 30–508（479 aa）
Chain B 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；TBS, 0.2um filtered
cryo-EM vitrification conditions Cryogen ETHANE；Blot force: 0 Wait time: 10s Blot time: 3-7s
Resolution 3.30 Å
7MXE Ab1245 Fab in complex with BG505 SOSIP.664 and 8ANC195 Fab Deposited 2021-05-19 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 × 14 PDB declaration: tetradecameric
Chain C 509–661（153 aa）
Chain D 509–661（153 aa）
Chain F 509–661（153 aa）
Chain G 32–508（477 aa）
Chain J 32–508（477 aa）
Chain P 32–508（477 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；0 blot force, 3 second blot time, 3 uL sample added
Resolution 3.70 Å
7RAI Cryo-EM structure of M4008_N1 Fab in complex with BG505 DS-SOSIP.664 Env trimer Deposited 2021-07-01 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 × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa）
Chain B 509–661（153 aa）
Chain C 30–505（476 aa）
Chain D 509–661（153 aa）
Chain E 30–505（476 aa）
Chain F 509–661（153 aa）
Mutation：I200C, T330N, A430C, A498C Mutation：I556P, T602C Mutation：I200C, T330N, A430C, A498C Mutation：I556P, T602C Mutation：I200C, T330N, A430C, A498C Mutation：I556P, T602C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.24 Å
7SQ1 BG505.MD39TS Env trimer in complex with Fab from antibody C05 Deposited 2021-11-04 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 × 10 PDB declaration: decameric
Chain B 509–661（153 aa）
Chain C 31–502（472 aa）
Chain D 509–661（153 aa）
Chain E 31–502（472 aa）
Chain F 509–661（153 aa）
Chain G 31–502（472 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 41 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7T9B ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs Deposited 2021-12-18 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 × 14 PDB declaration: tetradecameric
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 × 41 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
7TFN Cryo-EM structure of CD4bs antibody Ab1303 in complex with HIV-1 Env trimer BG505 SOSIP.664 Deposited 2022-01-06 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 × 12 PDB declaration: dodecameric
Chain X 509–661（153 aa） Fragment：UNP residues 509-661
Chain Y 509–661（153 aa） Fragment：UNP residues 509-661
Chain Z 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 MAN alpha-D-mannopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7TFO Cryo-EM structure of HIV-1 Env trimer BG505 SOSIP.664 in complex with CD4bs antibody Ab1573 Deposited 2022-01-06 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 × 12 PDB declaration: dodecameric
Chain X 509–661（153 aa） Fragment：UNP residues 509-661
Chain Y 509–661（153 aa） Fragment：UNP residues 509-661
Chain Z 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7TXD Cryo-EM structure of BG505 SOSIP HIV-1 Env trimer in complex with CD4 receptor (D1D2) and broadly neutralizing darpin bnD.9 Deposited 2022-02-08 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 × 12 PDB declaration: dodecameric
Chain A 30–505（476 aa）
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–505（476 aa）
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–505（476 aa）
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
7UCF Structure of the BG505 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24 Deposited 2022-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 29–505（477 aa） Fragment：UNP residues 29-505
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 FUC alpha-L-fucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M Bis-Tris pH 6.5, 20% PEG1500
Resolution 4.00 Å R-free 0.277
7UOJ The CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP.664 Deposited 2022-04-13 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 A 30–505（476 aa）
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 30–505（476 aa）
Chain I 30–505（476 aa）
Chain J 509–661（153 aa） Fragment：UNP residues 509-661
Mutation：T330N,A498C Mutation：I556P,T602C Mutation：I556P,T602C Mutation：T330N,A498C Mutation：T330N,A498C Mutation：I556P,T602C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；Phosphate buffered saline
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
8DP1 Cryo-EM structure of HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab Deposited 2022-07-14 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 × 12 PDB declaration: dodecameric
Chain B 30–505（476 aa） Fragment：gp120
Chain H 509–661（153 aa） Fragment：UNP residues 509-661
Chain J 30–505（476 aa） Fragment：gp120
Chain Q 509–661（153 aa） Fragment：UNP residues 509-661
Chain S 509–661（153 aa） Fragment：UNP residues 509-661
Chain W 30–505（476 aa） Fragment：gp120
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
8E1P Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs Deposited 2022-08-11 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: octadecameric
Chain X 509–661（153 aa） Fragment：UNP residues 509-661
Chain Y 509–661（153 aa） Fragment：UNP residues 509-661
Chain Z 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5, 12% w/v PEG8000
Resolution 3.82 Å R-free 0.301
8EUU Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB Deposited 2022-10-19 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 × 12 PDB declaration: dodecameric
Chain A 30–510（481 aa） Fragment：UNP residues 30-510
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–510（481 aa） Fragment：UNP residues 30-510
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–510（481 aa） Fragment：UNP residues 30-510
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8EUV Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB Deposited 2022-10-19 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 × 12 PDB declaration: dodecameric
Chain A 30–510（481 aa） Fragment：UNP residues 30-510
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–510（481 aa） Fragment：UNP residues 30-510
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–510（481 aa） Fragment：UNP residues 30-510
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8EUW Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-MM28 FAB Deposited 2022-10-19 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 × 12 PDB declaration: dodecameric
Chain A 30–510（481 aa） Fragment：UNP residues 30-510
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–510（481 aa） Fragment：UNP residues 30-510
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–510（481 aa） Fragment：UNP residues 30-510
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
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 2.70 Å
8FIS Structure of Bispecific CAP256V2LS-J3 Fab in complex with BG505 DS-SOSIP.664 Deposited 2022-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric
Chain A 509–661（153 aa） Fragment：UNP residues 509-661
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–510（481 aa） Fragment：UNP residues 30-510
Chain E 509–661（153 aa） Fragment：UNP residues 509-661
Chain F 30–510（481 aa） Fragment：UNP residues 30-510
Chain G 30–510（481 aa） Fragment：UNP residues 30-510
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
8FK5 Cryo-EM Structure of PG9RSH DU011 Fab in complex with BG505 DS-SOSIP.664 Deposited 2022-12-20 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 × 8 PDB declaration: octameric
Chain A 509–661（153 aa） Fragment：UNP residues 509-661
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–510（481 aa） Fragment：UNP residues 30-510
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 30–510（481 aa） Fragment：UNP residues 30-510
Chain I 30–510（481 aa） Fragment：UNP residues 30-510
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8FL1 Cryo-EM Structure of PG9RSH DU025 Fab in complex with BG505 DS-SOSIP.664 Deposited 2022-12-21 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 × 8 PDB declaration: octameric
Chain A 509–661（153 aa） Fragment：UNP residues 509-661
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–510（481 aa） Fragment：UNP residues 30-510
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 30–510（481 aa） Fragment：UNP residues 30-510
Chain I 30–510（481 aa） Fragment：UNP residues 30-510
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 40 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
8FLW Cryo-EM Structure of PGT145 DU303 Fab in complex with BG505 DS-SOSIP.664 Deposited 2022-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain A 509–661（153 aa） Fragment：UNP residues 509-661
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–510（481 aa） Fragment：UNP residues 30-510
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 30–510（481 aa） Fragment：UNP residues 30-510
Chain I 30–510（481 aa） Fragment：UNP residues 30-510
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
8FR6 Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP Deposited 2023-01-06 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 × 12 PDB declaration: dodecameric
Chain C 30–502（473 aa）
Chain G 30–502（473 aa）
Chain I 30–502（473 aa）
Mutation：BG505 DS-SOSIP construct Mutation：BG505 DS-SOSIP construct Mutation：BG505 DS-SOSIP construct NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain D 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 × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8G4M Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP Deposited 2023-02-10 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 × 12 PDB declaration: dodecameric
Chain C 30–502（473 aa）
Chain G 30–502（473 aa）
Chain I 30–502（473 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS + 0.005%(w/v) DDM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
8G4T Vaccine-elicited human antibody 2C09 in complex with HIV-1 envelope trimer BG505 DS-SOSIP Deposited 2023-02-10 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 × 12 PDB declaration: dodecameric
Chain C 30–502（473 aa）
Chain G 30–502（473 aa）
Chain I 30–502（473 aa）
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；PBS + 0.1mM DDM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
8G85 vFP52.02 Fab in complex with BG505 DS-SOSIP Env trimer Deposited 2023-02-17 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 × 12 PDB declaration: dodecameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain D 30–510（481 aa） Fragment：UNP residues 30-510
Chain E 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 30–510（481 aa） Fragment：UNP residues 30-510
Chain J 30–510（481 aa） Fragment：UNP residues 30-510
Chain K 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.99 Å
8G9W Cryo-EM structure of vFP49.02 Fab in complex with HIV-1 Env BG505 DS-SOSIP.664 (conformation 1) Deposited 2023-02-22 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 × 8 PDB declaration: octameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–510（481 aa） Fragment：UNP residues 30-510
Chain G 30–510（481 aa） Fragment：UNP residues 30-510
Chain O 509–661（153 aa） Fragment：UNP residues 509-661
Chain P 30–510（481 aa） Fragment：UNP residues 30-510
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
8G9X Cryo-EM structure of vFP49.02 Fab in complex with HIV-1 Env BG505 DS-SOSIP.664 (conformation 2) Deposited 2023-02-22 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 × 8 PDB declaration: octameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–510（481 aa） Fragment：UNP residues 30-510
Chain G 30–510（481 aa） Fragment：UNP residues 30-510
Chain O 509–661（153 aa） Fragment：UNP residues 509-661
Chain P 30–510（481 aa） Fragment：UNP residues 30-510
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.46 Å
8G9Y Cryo-EM structure of vFP49.02 Fab in complex with HIV-1 Env BG505 DS-SOSIP.664 (conformation 3) Deposited 2023-02-22 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 × 8 PDB declaration: octameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–510（481 aa） Fragment：UNP residues 30-510
Chain G 30–510（481 aa） Fragment：UNP residues 30-510
Chain O 509–661（153 aa） Fragment：UNP residues 509-661
Chain P 30–510（481 aa） Fragment：UNP residues 30-510
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
8GAS vFP48.02 Fab in complex with BG505 DS-SOSIP Env trimer Deposited 2023-02-23 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 × 12 PDB declaration: dodecameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain D 30–505（476 aa） Fragment：UNP residues 30-505
Chain E 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 30–505（476 aa） Fragment：UNP residues 30-505
Chain J 30–505（476 aa） Fragment：UNP residues 30-505
Chain K 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.04 Å
8SW3 BG505 GT1.1 SOSIP in complex with NHP Fabs 12C11 and RM20A3 Deposited 2023-05-17 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 E 509–661（153 aa） Fragment：UNP residues 509-661
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Mutation：I559P, T605C Mutation：I559P, T605C Mutation：I559P, T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent added shortly before freezing
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8SW4 BG505 GT1.1 SOSIP in complex with NHP Fabs 21N13, 21M20 and RM20A3 Deposited 2023-05-17 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 × 20 PDB declaration: eicosameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 509–661（153 aa） Fragment：UNP residues 509-661
Chain I 509–661（153 aa） Fragment：UNP residues 509-661
Mutation：I559P, T605C Mutation：I559P, T605C Mutation：I559P, T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Detergent added shortly before freezing
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8TGO Crystal structure of the BG505 triple tandem trimer gp140 HIV-1 Env in complex with PGT124 and 35O22 Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain G 30–504（475 aa） Fragment：UNP residues 30-504
Chain H 509–661（153 aa） Fragment：UNP residues 509-661
Chain R 30–504（475 aa） Fragment：UNP residues 30-504
Chain a 509–661（153 aa） Fragment：UNP residues 509-661
Chain e 30–504（475 aa） Fragment：UNP residues 30-504
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.1 M sodium acetate, 0.2 M zinc acetate, 11.5 % w/v PEG3000, pH 4.83
Resolution 5.75 Å R-free 0.292
8TJR CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO HERH-a.01 FAB Deposited 2023-07-24 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 × 10 PDB declaration: decameric
Chain A 30–504（475 aa）
Chain B 30–504（475 aa）
Chain C 30–504（475 aa）
Chain D 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 × 48 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.29 Å
8TJS CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO GPZ6-a.01 FAB Deposited 2023-07-24 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 × 12 PDB declaration: 12-meric
Chain B 509–661（153 aa）
Chain G 30–502（473 aa）
Chain H 509–661（153 aa）
Chain I 509–661（153 aa）
Chain N 30–502（473 aa）
Chain O 30–502（473 aa）
Mutation：I556P, T602C Mutation：I556P, T602C Mutation：I556P, T602C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8TNG Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing llama nanobody R27 targeting the CD4-binding site Deposited 2023-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–505（476 aa） Fragment：UNP residues 30-505
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–505（476 aa） Fragment：UNP residues 30-505
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
8TNH Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing llama nanobody G36 targeting the CD4-binding site Deposited 2023-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–505（476 aa） Fragment：UNP residues 30-505
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–505（476 aa） Fragment：UNP residues 30-505
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8TNI Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing bi-specific antibody CAP256L-R27 targeting the CD4-binding site and the V2-apex Deposited 2023-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–505（476 aa） Fragment：UNP residues 30-505
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–505（476 aa） Fragment：UNP residues 30-505
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.61 Å
8TOP Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide Deposited 2023-08-03 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 × 24 PDB declaration: 24-meric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 509–661（153 aa） Fragment：UNP residues 509-661
Chain C 30–505（476 aa） Fragment：UNP residues 30-505
Chain D 509–661（153 aa） Fragment：UNP residues 509-661
Chain E 30–505（476 aa） Fragment：UNP residues 30-505
Chain F 509–661（153 aa） Fragment：UNP residues 509-661
Chain O 30–505（476 aa） Fragment：UNP residues 30-505
Chain P 509–661（153 aa） Fragment：UNP residues 509-661
Chain Q 30–505（476 aa） Fragment：UNP residues 30-505
Chain R 509–661（153 aa） Fragment：UNP residues 509-661
Chain S 30–505（476 aa） Fragment：UNP residues 30-505
Chain T 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 82 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
8TOX Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab Deposited 2023-08-04 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 × 12 PDB declaration: dodecameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 30–504（475 aa）
Chain F 509–661（153 aa）
Chain G 30–504（475 aa）
Chain I 30–504（475 aa）
Mutation：A517E, M535N, N543Q, T569G, I573F, R588E, D589V, S636G, N651F, K655I Mutation：A517E, M535N, N543Q, T569G, I573F, R588E, D589V, S636G, N651F, K655I Mutation：A517E, M535N, N543Q, T569G, I573F, R588E, D589V, S636G, N651F, K655I NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS with 0.1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 13-meric
Chain A 30–505（476 aa）
Chain E 30–505（476 aa）
Chain J 30–505（476 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 30–510（481 aa）
Chain E 30–510（481 aa）
Chain I 30–510（481 aa）
Mutation：A501C T332N E509R K510R A512R V513R Mutation：A501C T332N E509R K510R A512R V513R Mutation：A501C T332N E509R K510R A512R V513R 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 32–501（470 aa）
Chain C 32–501（470 aa）
Chain E 32–501（470 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 32–501（470 aa）
Chain C 32–501（470 aa）
Chain E 32–501（470 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 32–501（470 aa）
Chain C 32–501（470 aa）
Chain E 32–501（470 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 14-meric
Chain A 32–501（470 aa）
Chain C 32–501（470 aa）
Chain E 32–501（470 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
8VFV HIV Env BG505_MD39_B16 SOSIP boosting trimer in complex with B16_d77.5 mouse Fab and RM20A3 Fab Deposited 2023-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 30–510（481 aa）
Chain B 509–661（153 aa）
Chain E 30–510（481 aa）
Chain F 509–661（153 aa）
Chain J 30–510（481 aa）
Chain K 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9AUG Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R Deposited 2024-02-29 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 × 12 PDB declaration: 12-meric
Chain A 30–495（466 aa） Fragment：d949.GS-gp120
Chain B 30–495（466 aa） Fragment：d949.GS-gp120
Chain C 30–495（466 aa） Fragment：d949.GS-gp120
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
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9AUH Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3 Deposited 2024-02-29 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 × 12 PDB declaration: 12-meric
Chain A 30–495（466 aa） Fragment：d949.GS-gp120
Chain B 30–495（466 aa） Fragment：d949.GS-gp120
Chain C 30–495（466 aa） Fragment：d949.GS-gp120
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
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9AUI Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA4 Deposited 2024-02-29 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 × 12 PDB declaration: 12-meric
Chain A 30–495（466 aa） Fragment：d949.GS-gp120
Chain B 30–495（466 aa） Fragment：d949.GS-gp120
Chain C 30–495（466 aa） Fragment：d949.GS-gp120
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
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9AXD HIV BG505.v5.2 (N289/N241) SOSIP Env in Complex with gp120-Interface pAb from Rh.33203 Deposited 2024-03-06 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 × 8 PDB declaration: octameric
Chain A 30–508（479 aa）
Chain B 507–661（155 aa）
Chain C 30–508（479 aa）
Chain D 507–661（155 aa）
Chain E 30–508（479 aa）
Chain F 507–661（155 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 40 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9AY6 HIV BG505.v5.2 (N289/N241) SOSIP Env in Complex with V5 pAb from Rh.33203 Deposited 2024-03-07 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 × 8 PDB declaration: octameric
Chain A 30–508（479 aa）
Chain B 507–661（155 aa）
Chain C 30–508（479 aa）
Chain D 507–661（155 aa）
Chain E 30–508（479 aa）
Chain F 507–661（155 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9AYS HIV BG505.v5.2 (N289/N241) SOSIP Env in Complex with V5, gp120-Interface, and Anti-Immune Complex pAbs from Rh.33203 Deposited 2024-03-08 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 × 12 PDB declaration: 12-meric
Chain A 30–508（479 aa）
Chain B 507–661（155 aa）
Chain C 30–508（479 aa）
Chain D 507–661（155 aa）
Chain E 30–508（479 aa）
Chain F 507–661（155 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 43 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9AYV HIV CH505/BG505 SOSIP.v8.1 Env in Complex with V1/V3 Epitope and Anti-Immune Complex pAbs from Rabbit 2474 Deposited 2024-03-08 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 × 10 PDB declaration: decameric
Chain B 507–661（155 aa）
Chain D 507–661（155 aa）
Chain F 507–661（155 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
9B8B RM038 Fab in complex with Apex-GT 6.2 trimer and RM20A3 Fab Deposited 2024-03-29 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 × 14 PDB declaration: tetradecameric
Chain A 30–505（476 aa）
Chain B 509–661（153 aa）
Chain C 30–505（476 aa）
Chain D 30–505（476 aa）
Chain E 509–661（153 aa）
Chain F 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 49 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B8C RM018 Fab in complex with Apex GT 6.2 trimer and RM20A3 Fab Deposited 2024-03-29 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 × 14 PDB declaration: tetradecameric
Chain A 30–504（475 aa）
Chain B 509–661（153 aa）
Chain C 30–504（475 aa）
Chain D 30–504（475 aa）
Chain E 509–661（153 aa）
Chain F 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9BNK Cryo-EM structure of rhesus antibody V031-a.01 in complex with HIV-1 Env BG505 DS-SOSIP Deposited 2024-05-02 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 × 8 PDB declaration: octameric
Chain A 515–661（147 aa）
Chain B 515–661（147 aa）
Chain C 515–661（147 aa）
Chain E 31–503（473 aa）
Chain F 31–503（473 aa）
Chain G 31–503（473 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9BNM Cryo-EM structure of rhesus antibody 44715-a.01 in complex with HIV-1 Env BG505 DS-SOSIP Deposited 2024-05-02 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 × 8 PDB declaration: octameric
Chain A 30–505（476 aa）
Chain B 30–505（476 aa）
Chain C 30–505（476 aa）
Chain X 510–661（152 aa）
Chain Y 510–661（152 aa）
Chain Z 510–661（152 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
9BNP Cryo-EM structure of rhesus antibody V033-a.01 in complex with HIV-1 Env BG505 DS-SOSIP Deposited 2024-05-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain A 32–502（471 aa）
Chain B 517–661（145 aa）
Chain E 32–502（471 aa）
Chain F 517–661（145 aa）
Chain I 32–502（471 aa）
Chain J 517–661（145 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 3.17 Å
9BTL Cryo-EM structure of rhesus antibody 41328-a.01 in complex with HIV-1 Env BG505 DS-SOSIP Deposited 2024-05-15 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 × 8 PDB declaration: octameric
Chain A 30–505（476 aa）
Chain B 510–661（152 aa）
Chain E 30–505（476 aa）
Chain F 510–661（152 aa）
Chain I 30–505（476 aa）
Chain J 510–661（152 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 2.96 Å
9CF5 STRUCTURE OF CD4 MIMETIC CJF-III-288 IN COMPLEX WITH BG505 SOSIP.664 HIV-1ENV TRIMER AND 17B FAB Deposited 2024-06-27 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 × 12 PDB declaration: dodecameric
Chain A 32–508（477 aa）
Chain B 509–661（153 aa） Fragment：residues 512-664 (509-661 Uniprot numbering)
Chain C 32–508（477 aa）
Chain D 509–661（153 aa） Fragment：residues 512-664 (509-661 Uniprot numbering)
Chain E 32–508（477 aa）
Chain F 509–661（153 aa） Fragment：residues 512-664 (509-661 Uniprot numbering)
Mutation：T332N, A501C, E509R, K510R, insertion of RR after residue 511 Mutation：I559P, T605C Mutation：T332N, A501C, E509R, K510R, insertion of RR after residue 511 Mutation：I559P, T605C Mutation：T332N, A501C, E509R, K510R, insertion of RR after residue 511 Mutation：I559P, T605C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 Y26 propyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9D1W Cryo-EM structure of PGDM1400 Fab bound to HIV-1 BG505 DS-SOSIP.664 Env trimer Deposited 2024-08-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 30–505（476 aa） Fragment：UNP residues 30-505
Chain C 30–505（476 aa） Fragment：UNP residues 30-505
Chain a 509–661（153 aa） Fragment：UNP residues 509-661
Chain b 509–661（153 aa） Fragment：UNP residues 509-661
Chain c 509–661（153 aa） Fragment：UNP residues 509-661
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
9D3D Cryo-EM structure of PGT145 R100aS Fab bound to HIV-1 BG505 DS-SOSIP.664 Env trimer Deposited 2024-08-09 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 × 8 PDB declaration: octameric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain B 30–505（476 aa） Fragment：UNP residues 30-505
Chain C 30–505（476 aa） Fragment：UNP residues 30-505
Chain a 509–661（153 aa） Fragment：residues 512-664
Chain b 509–661（153 aa） Fragment：residues 512-664
Chain c 509–661（153 aa） Fragment：residues 512-664
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 509–661（153 aa） Fragment：UNP residues 509-611
Chain E 509–661（153 aa） Fragment：UNP residues 509-611
Chain F 509–661（153 aa） Fragment：UNP residues 509-611
Mutation：I559P,T605C Mutation：I559P,T605C Mutation：I559P,T605C 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
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric
Chain F 30–509（480 aa）
Chain K 30–509（480 aa）
Chain L 30–509（480 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
9MI0 61-12A01 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab Deposited 2024-12-12 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 × 18 PDB declaration: octadecameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-611
Chain D 509–661（153 aa） Fragment：UNP residues 509-611
Chain F 509–661（153 aa） Fragment：UNP residues 509-611
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 2.80 Å
9MIA 206-3G08 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab Deposited 2024-12-12 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 × 18 PDB declaration: octadecameric
Chain B 509–661（153 aa） Fragment：UNP residues 509-611
Chain D 509–661（153 aa） Fragment：UNP residues 509-611
Chain F 509–661（153 aa） Fragment：UNP residues 509-611
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9MIB 206-9C09 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab Deposited 2024-12-12 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 18-meric
Chain B 509–661（153 aa） Fragment：UNP residues 509-611
Chain D 509–661（153 aa） Fragment：UNP residues 509-611
Chain F 509–661（153 aa） Fragment：UNP residues 509-611
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9MIH 273-4D01 Fab in complex with HIV-1 BG505 SOSIP Env trimer and RM20A3 Fab Deposited 2024-12-12 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 × 14 PDB declaration: 14-meric
Chain A 30–505（476 aa）
Chain B 509–661（153 aa）
Chain C 30–505（476 aa）
Chain D 509–661（153 aa）
Chain E 30–505（476 aa）
Chain F 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 44 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9MII 253-7A03 Fab in complex with HIV-1 BG505 SOSIP Env trimer and RM20A3 Fab Deposited 2024-12-12 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 × 14 PDB declaration: 14-meric
Chain A 30–505（476 aa）
Chain B 509–661（153 aa）
Chain C 30–505（476 aa）
Chain D 509–661（153 aa）
Chain E 30–505（476 aa）
Chain F 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 44 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9MQG RM017 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab Deposited 2025-01-03 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 × 14 PDB declaration: tetradecameric
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 × 39 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9O2Q BG505-DS SOSIP in complex with 007 bNAb Fabs - Class 0 (unbound) Deposited 2025-04-04 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 Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 32–507（476 aa）
Chain B 508–661（154 aa）
Chain C 32–507（476 aa）
Chain D 508–661（154 aa）
Chain E 32–507（476 aa）
Chain F 508–661（154 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；3s blot, 0 blot force
Resolution 2.90 Å
9O2R BG505-DS SOSIP in complex with 007 bNAb Fabs - Class 1 (1 Fab bound) Deposited 2025-04-04 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 × 8 PDB declaration: octameric
Chain A 32–507（476 aa）
Chain B 508–661（154 aa）
Chain C 32–507（476 aa）
Chain D 508–661（154 aa）
Chain E 32–507（476 aa）
Chain F 508–661（154 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；3s blot, 0 blot force
Resolution 3.00 Å
9O2S BG505-DS SOSIP in complex with 007 bNAb Fabs - Class 2 (2 Fabs bound) Deposited 2025-04-04 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 × 10 PDB declaration: decameric
Chain A 32–507（476 aa）
Chain B 508–661（154 aa）
Chain C 32–507（476 aa）
Chain D 508–661（154 aa）
Chain E 32–507（476 aa）
Chain F 508–661（154 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；3s blot, 0 blot force
Resolution 3.20 Å
9O2T BG505-DS SOSIP in complex with 007 bNAb Fabs - Class 3 (3 Fabs bound) Deposited 2025-04-04 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 × 12 PDB declaration: dodecameric
Chain A 32–507（476 aa）
Chain B 508–661（154 aa）
Chain C 32–507（476 aa）
Chain D 508–661（154 aa）
Chain E 32–507（476 aa）
Chain F 508–661（154 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；3s blot, 0 blot force
Resolution 3.40 Å
9O2U BG505 SOSIP in complex with 007 bNAb IgG1 - trimer-dimer class Deposited 2025-04-04 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 × 24 PDB declaration: 24-meric
Chain A 32–507（476 aa）
Chain B 508–661（154 aa）
Chain C 32–507（476 aa）
Chain D 508–661（154 aa）
Chain E 32–507（476 aa）
Chain F 508–661（154 aa）
Chain O 32–507（476 aa）
Chain P 508–661（154 aa）
Chain Q 32–507（476 aa）
Chain R 508–661（154 aa）
Chain S 32–507（476 aa）
Chain T 508–661（154 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9O8M Ab1983 in complex with HIV-1 Env variant WIN332 Deposited 2025-04-16 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 × 10 PDB declaration: decameric
Chain E 32–510（479 aa）
Chain F 509–661（153 aa）
Chain I 32–510（479 aa）
Chain J 509–661（153 aa）
Chain K 32–510（479 aa）
Chain L 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.79 Å
9OED Ab1999 in complex with HIV-1 Env RC1 Deposited 2025-04-28 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 × 8 PDB declaration: octameric
Chain D 509–661（153 aa）
Chain F 509–661（153 aa）
Chain J 509–661（153 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；1X PBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.94 Å
9OGM BG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 and VRC01 Fabs (1x 10E8 Fab) Deposited 2025-05-01 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 × 17 PDB declaration: 17-meric
Chain A 30–504（475 aa）
Chain B 30–504（475 aa）
Chain C 30–504（475 aa）
Not recorded 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
9OGT HIV-1 Env BG505 SOSIP.664-His in complex with PGT122 and 3BNC117 Fabs Deposited 2025-05-01 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: 18-meric
Chain A 30–505（476 aa）
Chain C 30–505（476 aa）
Chain E 30–505（476 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9OGU HIV-1 Env BG505 SOSIP.664-dPG-His in complex with PGT122 and 3BNC117 Fabs Deposited 2025-05-01 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: 18-meric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain C 30–505（476 aa） Fragment：UNP residues 30-505
Chain E 30–505（476 aa） Fragment：UNP residues 30-505
Mutation：T332N, A501C Mutation：T332N, A501C Mutation：T332N, A501C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 18-meric
Chain B 509–661（153 aa）
Chain D 509–661（153 aa）
Chain F 509–661（153 aa）
Mutation：F516S, I556P, S558P, L565D, V567H, R582H, T602C Mutation：F516S, I556P, S558P, L565D, V567H, R582H, T602C Mutation：F516S, I556P, S558P, L565D, V567H, R582H, T602C 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 18-meric
Chain B 509–661（153 aa）
Chain D 509–661（153 aa）
Chain F 509–661（153 aa）
Mutation：F516S, I556P, S558P, L565D, V567H, R582H, T602C Mutation：F516S, I556P, S558P, L565D, V567H, R582H, T602C Mutation：F516S, I556P, S558P, L565D, V567H, R582H, T602C 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
9PNI Cryo-EM structure of J601-1B2 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer Deposited 2025-07-21 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 × 12 PDB declaration: 12-meric
Chain C 30–502（473 aa）
Chain G 30–502（473 aa）
Chain I 30–502（473 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 MAN alpha-D-mannopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer supplemented with 0.1 mM DDM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
9PNN Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer Deposited 2025-07-21 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 × 12 PDB declaration: 12-meric
Chain C 30–502（473 aa）
Chain G 30–502（473 aa）
Chain I 30–502（473 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS + 0.005% (w/v) DDM
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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 30–505（476 aa） Fragment：UNP residues 30-505
Chain C 30–505（476 aa） Fragment：UNP residues 30-505
Chain E 30–505（476 aa） Fragment：UNP residues 30-505
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
9YHO AJ09-21 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-09-30 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 × 12 PDB declaration: dodecameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9YHQ AJ09-83 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-09-30 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 × 12 PDB declaration: dodecameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9YHR AJ09-110 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-09-30 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 × 12 PDB declaration: dodecameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9YHS AM12-340 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-09-30 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 × 12 PDB declaration: dodecameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.30 Å
9YHT AM12-347 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-09-30 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 × 12 PDB declaration: dodecameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9YIB AM12-351 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 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 E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9YID AM12-352 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 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 E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
9YIE NN39-25 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 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 E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9YIF NN39-171 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 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 E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9YIG V634-136 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 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 E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9YIH V634-136 UCA Fab in complex with HIV-1 Env del4-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9YII V645-158 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9YIJ HIV-1 Env 5MUT-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9YIK HIV-1 Env del4-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–508（477 aa）
Chain F 32–508（477 aa）
Chain G 32–508（477 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9YIL HIV-1 Env del8-3fill SOSIP Deposited 2025-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 509–661（153 aa）
Chain B 509–661（153 aa）
Chain C 509–661（153 aa）
Chain E 32–510（479 aa）
Chain F 32–510（479 aa）
Chain G 32–510（479 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；150 mM NaCl, 20 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å

186 other PDB entries and 199 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q2N0S6_9HIV1
Isoform —
PDB entities 1, 4
Chains and sequence ranges Author chain B； PDBConstruct 1–153； UniProt 509–661 Author chain G； PDBConstruct 1–475； UniProt 30–504

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

SAXS scattering curve SAXS Profile

SAXS profile for 6w03

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6w03
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6w03
Deposition date deposition_date2020-02-28
Structure title titleCrystal Structure of HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.3 Angstrom
Keywords keywordsHIV-1 Envelope Prefusion Trimer, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier52.53 Å
Radius of gyration Rg (electron density) rg_electron53.82 Å
Forward intensity I(0) i0313143000.00
Molecular weight molecular_weight143920.0 kDa
Excluded volume excluded_volume179320 ų
Envelope volume envelope_volume262320 ų
Hydration-shell volume shell_volume47375 ų
Envelope diameter envelope_diameter192.8 Å
Shell Rg shell_rg45.35 Å
Envelope Rg envelope_rg53.81 Å
Shape Rg shape_rg53.84 Å
Total Rg total_rg53.40 Å
Total atoms total_atoms10096
Residues n_residues1178
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax182.1 Å
Rg (real space) rg_real53.32 Å
Rg uncertainty (real space) rg_real_error2.73 Å
I(0) (real space) i0_real3.1310e+08
I(0) uncertainty (real space) i0_real_error6.5600e+06
Rg (reciprocal space) rg_reciprocal51.86 Å
I(0) (reciprocal space) i0_reciprocal312500000.0000
Solution quality estimate total_estimate0.4768
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4 Å
Skewness Skewness skewness0.643
Kurtosis Kurtosis kurtosis-0.338
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13760000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.522; Stabil: 1.000; Sysdev: 0.007; Positv: 1.000; Valcen: 0.525; Smooth: 0.082
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (13)

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6w03d_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6w03e_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6w03h1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6w03h2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6w03l1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6w03l2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id6w03E00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6w03H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6w03H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6w03L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6w03L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)