6nqd

Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab

Method: ELECTRON MICROSCOPY D_max: 138.7 Å Quality: REASONABLE

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

T/F100 Env 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 33 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 29–508 Chain B； UniProt 513–665 Chain E； UniProt 29–508 Chain F； UniProt 513–665 Chain I； UniProt 29–508 Chain J； UniProt 513–665	Fragment：UNP residues 29-508 Fragment：UNP residues 513-665	8ANC195 G52K5 heavy chain, IG gamma-1 chain × 3 （S6B2A6） 8ANC195 G52K5 light chain × 3 （P0DOX7） ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 21 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 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 6NQD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8DOK Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 and 10-1074 Deposited 2022-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 29–508（480 aa） Fragment：UNP residues 29-508 Chain E 29–508（480 aa） Fragment：UNP residues 29-508 Chain I 29–508（480 aa） Fragment：UNP residues 29-508	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 3.20 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A140EMT3_9HIV1
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–480； UniProt 29–508 Author chain E； PDBConstruct 1–480； UniProt 29–508 Author chain I； PDBConstruct 1–480； UniProt 29–508 Author chain B； PDBConstruct 1–153； UniProt 513–665 Author chain F； PDBConstruct 1–153； UniProt 513–665 Author chain J； PDBConstruct 1–153； UniProt 513–665

8ANC195 G52K5 heavy chain, IG gamma-1 chain

Homo sapiens

UniProt S6B2A6

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 33 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain C； UniProt 145–251 Chain G； UniProt 145–251 Chain K； UniProt 145–251	Not recorded	T/F100 Env gp120 × 3 （A0A140EMT3） T/F100 Env gp41 × 3 （A0A140EMT3） 8ANC195 G52K5 light chain × 3 （P0DOX7） ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 21 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6NQD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5W0D Inferred precursor (UCA) of the human antibody lineage K03.12 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006 Deposited 2017-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 145–249（105 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；200 mM sodium chloride, 100 mM PIPES, pH 6.0, 20% w/v PEG2000 MME	Resolution 1.90 Å R-free 0.234
6BKD Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3D Deposited 2017-11-08	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 H 134–247（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% (w/v) PEG 6000, 0.1M Hepes, pH 7.0	Resolution 3.25 Å R-free 0.286

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S6B2A6_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 133–239； UniProt 145–251 Author chain G； PDBConstruct 133–239； UniProt 145–251 Author chain K； PDBConstruct 133–239； UniProt 145–251

8ANC195 G52K5 light chain

Homo sapiens

UniProt P0DOX7

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 33 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain D； UniProt 109–214 Chain H； UniProt 109–214 Chain L； UniProt 109–214	Not recorded	T/F100 Env gp120 × 3 （A0A140EMT3） T/F100 Env gp41 × 3 （A0A140EMT3） 8ANC195 G52K5 heavy chain, IG gamma-1 chain × 3 （S6B2A6） ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 21 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6NQD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NM4 Crystal structure of broadly neutralizing antibody CR8043 Deposited 2013-11-14	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 × 2 PDB declaration: dimeric	Chain L 115–214（100 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；20% PEG 6000, 0.1 M HEPES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.65 Å R-free 0.232
4NM4 Crystal structure of broadly neutralizing antibody CR8043 Deposited 2013-11-14	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 × 2 PDB declaration: dimeric	Chain M 115–214（100 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；20% PEG 6000, 0.1 M HEPES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.65 Å R-free 0.232
4NM8 Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin Deposited 2013-11-14	Different construct 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 L 115–214（100 aa） Chain M 115–214（100 aa） Chain N 115–214（100 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；2.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5, 3% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 4.00 Å R-free 0.292
5VIC Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII Deposited 2017-04-14	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 × 3 PDB declaration: trimeric	Chain L 109–214（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.1M sodium acetate trihydrate pH 4.5, 30% w/v PEG 1500	Resolution 3.00 Å R-free 0.286
5VIG Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII Deposited 2017-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 109–214（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；10% isopropanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 26% PEG 400	Resolution 3.00 Å R-free 0.257
5VIG Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII Deposited 2017-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 109–214（106 aa）	Not recorded	FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；10% isopropanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 26% PEG 400	Resolution 3.00 Å R-free 0.257
5W1K JUNV GP1 CR1-10 Fab CR1-28 Fab complex Deposited 2017-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 109–212（104 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.7；297 K；1.9 M AmSO4 pH 7.7	Resolution 3.99 Å R-free 0.288
5W1K JUNV GP1 CR1-10 Fab CR1-28 Fab complex Deposited 2017-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 109–212（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.7；297 K；1.9 M AmSO4 pH 7.7	Resolution 3.99 Å R-free 0.288
5W1K JUNV GP1 CR1-10 Fab CR1-28 Fab complex Deposited 2017-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 109–212（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.7；297 K；1.9 M AmSO4 pH 7.7	Resolution 3.99 Å R-free 0.288
5W1K JUNV GP1 CR1-10 Fab CR1-28 Fab complex Deposited 2017-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 109–212（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.7；297 K；1.9 M AmSO4 pH 7.7	Resolution 3.99 Å R-free 0.288
6BF7 Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy chain, FAB H11-E light chain Deposited 2017-10-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 129–211（83 aa） Chain F 129–211（83 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；The cryo grids were made using Spotiton	Resolution 6.50 Å
6BF9 Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy chain, FAB H11-E light chain Deposited 2017-10-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 109–211（103 aa） Chain F 109–211（103 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；The cryo grids were made using Spotiton	Resolution 7.20 Å
6MSY Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement Deposited 2018-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 109–213（105 aa）	Not recorded	UNX UNKNOWN LIGAND × 8 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；295 K；27% Peg 4000, 0.05M sodium acetate	Resolution 2.00 Å R-free 0.242
6MU3 Anti-HIV-1 Fab 2G12 + Man7 re-refinement 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 × 4 PDB declaration: tetrameric	Chain K 110–213（104 aa） Chain L 110–213（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；295 K；20% Peg 4000, 0.2M sodium tartrate	Resolution 2.33 Å R-free 0.234
6MUB Anti-HIV-1 Fab 2G12 + Man5 re-refinement 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 × 4 PDB declaration: tetrameric	Chain K 110–213（104 aa） Chain L 110–213（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；295 K；1.6M sodium/potassium phosphate	Resolution 2.50 Å R-free 0.280
6N2X Anti-HIV-1 Fab 2G12 + Man9 re-refinement Deposited 2018-11-14	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 × 4 PDB declaration: tetrameric	Chain K 109–213（105 aa） Chain L 109–213（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；25% Peg 400, 0.2M imidazole malate	Resolution 3.00 Å R-free 0.283
6N32 Anti-HIV-1 Fab 2G12 re-refinement Deposited 2018-11-14	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 × 4 PDB declaration: tetrameric	Chain L 109–213（105 aa） Chain M 109–213（105 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；1.05M ammonium sulfate, 18% Peg 6000, 0.1M imidazole malate	Resolution 2.20 Å R-free 0.227
6N35 Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement Deposited 2018-11-14	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 × 4 PDB declaration: tetrameric	Chain K 109–213（105 aa） Chain L 109–213（105 aa）	Not recorded	BEZ BENZOIC ACID × 1 GOL GLYCEROL × 1 MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；2M Sodium/Potassium Phosphate	Resolution 1.75 Å R-free 0.238
6UOE 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide Deposited 2019-10-14	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 × 3 PDB declaration: trimeric	Chain L 114–214（101 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M magnesium chloride, 13.4% PEG3350, 16.75% PEG400, 0.1 M Tris, pH 8.5	Resolution 1.80 Å R-free 0.186
6UTA Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII 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 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 109–214（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；% w/v tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium pH 7.0, 20% w/v polyethylene glycol 3,350	Resolution 3.10 Å R-free 0.291
6UTA Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII 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 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 109–214（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；% w/v tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium pH 7.0, 20% w/v polyethylene glycol 3,350	Resolution 3.10 Å R-free 0.291
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII 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 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 109–214（106 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII 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 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 109–214（106 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII 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 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 109–214（106 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII 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 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 109–214（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII 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 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 109–214（106 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
8BBO SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab Deposited 2022-10-14	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 × 3 PDB declaration: trimeric	Chain L 2–214（213 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2% (v/v) PEG400, 0.1M imidazole pH7.0 and 24% (w/v) PEG MME 5000.	Resolution 2.75 Å R-free 0.252
8XKJ Ckappa domain of human immunoglobulin Deposited 2023-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–213（104 aa） Fragment：Ckappa domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) Not defined；Pressure 1 NMR sample composition 1.0 mM [U-13C; U-15N] protein, 5 mM Napi, 50 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

18 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGK_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 110–215； UniProt 109–214 Author chain H； PDBConstruct 110–215； UniProt 109–214 Author chain L； PDBConstruct 110–215； UniProt 109–214

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6nqd
Deposition date deposition_date	2019-01-21
Structure title title	Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab
Keywords keywords	HIV-1, Env, trimer, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	45.31 Å
Radius of gyration Rg (electron density) rg_electron	44.48 Å
Forward intensity I(0) i0	1232690000.00
Molecular weight molecular_weight	287620.0 kDa
Excluded volume excluded_volume	358360 Å³
Envelope volume envelope_volume	502090 Å³
Hydration-shell volume shell_volume	90246 Å³
Envelope diameter envelope_diameter	141.7 Å
Shell Rg shell_rg	52.51 Å
Envelope Rg envelope_rg	43.69 Å
Shape Rg shape_rg	44.47 Å
Total Rg total_rg	44.83 Å
Total atoms total_atoms	20175
Residues n_residues	2337
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	138.7 Å
Rg (real space) rg_real	44.97 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	1.2330e+09
I(0) uncertainty (real space) i0_real_error	2.2110e+07
Rg (reciprocal space) rg_reciprocal	45.31 Å
I(0) (reciprocal space) i0_reciprocal	1233000000.0000
Solution quality estimate total_estimate	0.6561
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.4 Å
Skewness Skewness skewness	0.030
Kurtosis Kurtosis kurtosis	-0.492
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	170500000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.971; Smooth: 0.828

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	T/F100 Env gp120
Molecular weight formula_weight	54739.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I
Atom count atom_count	20175

ATNNLWVTVYYGVPVWRDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEMHLKNVTENFNMWKNNMVEQMQEDVISLWDQSLKPCVKLTPLCVTLNCTSATVTNYTKVNDTSDIIGNITDDVRNCSFNMTTELRDKQQKVYALFYKLDIVPIDDSSNNGSSNFSEYRLINCNTSVIKQACPKVSFDPIPIHYCTPAGYAILRCNDKKFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEGIIIRSENLTNNAKTIIVHFNESVKINCTRPSNNTRTGIHIGPGQVFYKTGDIIGDIRKAYCNISGAQWHKVLGRVANKLKEHFNNKTIVFKPSSGGDPEITMHHFNCRGEFFYCNTTKLFNSTWGGNKNETRDNGTITIPCRIKQIINMWQGVGQAMYAPPIKGVIKCLSNITGILLTRDGGNDSTENNETFRPGGGNIKDNWRNELYKYKVVQIEPLGIAPTKCKRRVVERRRRRR

来源 Source

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

Entity 2 Entity 2 polymer

Description description	T/F100 Env gp41
Molecular weight formula_weight	20333.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

AVGLGAMIFGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAPEAQQHLLQLTVWGIKQLQARVLAVERYLQDQKFLGLWGCSGKIICCTAVPWNSSWSNKTFEEIWNNMTWIEWEREISNYTSQIYDILTISQTQQEKNEKDLLELDAAAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

来源 Source

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

Entity 3 Entity 3 polymer

Description description	8ANC195 G52K5 heavy chain, IG gamma-1 chain
Molecular weight formula_weight	26153.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K

QIHLVQSGTEVKKPGSSVTVSCKAYGVNTFGLYAVNWVRQAPGQSLEYIGQIWRWKSSASHHFRGRVLISAVDLTGSSPPISSLEIKNLTSDDTAVYFCTTTSTYDRWSGLHHDGVMAFSSWGQGTLISVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	8ANC195 G52K5 light chain
Molecular weight formula_weight	23460.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

DIQMTQSPSTLSASTGDTVRISCRASQSITGNWVAWYQQRPGKAPRLLIYRGAALLGGVPSRFRGSAAGTDFTLTIGNLQAEDFGTFYCQQYDTYPGTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1721.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 6 Entity 6 branched

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

Entity 7 Entity 7 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	21

Entity 8 Entity 8 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 9 Entity 9 branched

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

Entity 10 Entity 10 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	30

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6nqdC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6nqdG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6nqdK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	170716

fit	/app/data/saxs_computation/nq/6nqd/6nqd.fit
pddf	/app/data/pr_computation/nq/6nqd/6nqd.pr.out
profile	/app/data/saxs_computation/nq/6nqd/6nqd.dat

Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab

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

T/F100 Env gp120

State in the Current Structure

Other States of the Same Protein in the Database

8ANC195 G52K5 heavy chain, IG gamma-1 chain

State in the Current Structure

Other States of the Same Protein in the Database

8ANC195 G52K5 light chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 branched

Entity 10 Entity 10 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)