HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120
Human immunodeficiency virus 1
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Other combination Heteromer Protein × 12 其他Polymer 15 PDB declaration: dodecameric（12） Consistent with protein copy count | Chain A； UniProt 30–505 Chain B； UniProt 509–661 | Fragment：UNP residues 30-505 Mutation：T332N,A501C Mutation：I559P,T605C | RM20A3 Fab Heavy Chain × 3 RM20A3 Fab Light Chain × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ;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 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 |
| 2 | Other combination Heteromer Protein × 4 其他Polymer 5 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 30–505 Chain B； UniProt 509–661 | Fragment：UNP residues 30-505 Mutation：T332N,A501C Mutation：I559P,T605C | RM20A3 Fab Heavy Chain × 1 RM20A3 Fab Light Chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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 |
| 3 | Other combination Heteromer Protein × 4 其他Polymer 5 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 30–505 Chain B； UniProt 509–661 | Fragment：UNP residues 30-505 Mutation：T332N,A501C Mutation：I559P,T605C | RM20A3 Fab Heavy Chain × 1 RM20A3 Fab Light Chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 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 |
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 6X9S | 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 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 method 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 method 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 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 method 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 method 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 method 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 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 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
30–501（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 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：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 method 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 method 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 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）
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 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 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 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 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 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 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 method 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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain B
509–661（153 aa）
Fragment：UNP residues 509-661
Chain G
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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain B
509–661（153 aa）
Fragment：UNP residues 509-661
Chain G
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 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 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 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 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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 method 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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：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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
509–661（153 aa）
Fragment：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 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：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 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：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 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：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 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 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 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 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）
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 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）
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 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）
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 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 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 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 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 method 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
30–504（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 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 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 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 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 method 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 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 method 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 method 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 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 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 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 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 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 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 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 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）
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 |
| 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 Deposited 2020-02-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain B
509–661（153 aa）
Fragment：ectodomain
Chain G
30–504（475 aa）
|
Mutation：I559P, T605C Mutation：N137A, I201C, N302M, T320L, A329P, T332N, A433C, A501C | 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 |
| 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 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 ligand/ion 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 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 | Parsed fields agree | 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 | Parsed fields agree | 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 | Parsed fields agree | 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
509–661（153 aa）
Fragment：UNP residues 509-661
Chain G
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 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 ligand/ion 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 method 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 method 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 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 ligand/ion 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 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 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 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 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 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 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 conditions | 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 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 ligand/ion 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 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 18-meric |
Chain B
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 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 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 ligand/ion Different experimental conditions | 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 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 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 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 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 ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
509–661（153 aa）
Chain B
509–661（153 aa）
Chain C
509–661（153 aa）
Chain 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 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 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 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 ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
509–661（153 aa）
Chain B
509–661（153 aa）
Chain C
509–661（153 aa）
Chain 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 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 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 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 197 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | Q2N0S6_9HIV1 |
| Isoform | — |
| PDB entities | 1, 2 |
| Chains and sequence ranges | Author chain A； PDBConstruct 36–511； UniProt 30–505 Author chain B； PDBConstruct 1–153； UniProt 509–661 |
