← Back to search
3dnl

Molecular structure for the HIV-1 gp120 trimer in the b12-bound state

Method: ELECTRON MICROSCOPY Dmax: 133.9 Å Quality: REASONABLE
▼

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

HIV-1 envelope glycoprotein gp120

HIV-1 M:B_HXB2R

UniProt P04578

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count Chain A； UniProt 90–124 Chain B； UniProt 198–297 Chain B； UniProt 330–396 Chain C； UniProt 410–492 Chain D； UniProt 90–124 Chain E； UniProt 198–297 Chain E； UniProt 330–396 Chain F； UniProt 410–492 Chain G； UniProt 90–124 Chain H； UniProt 198–297 Chain H； UniProt 330–396 Chain I； UniProt 410–492 Fragment：Core: Residues 90-124 Fragment：Core: Residues 198-396 Fragment：Core: Residues 410-492 No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA；pH 7.2；0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA cryo-EM vitrification conditions：Cryogen ETHANE；Ethane 77K 100%RH Vitrobot Resolution 20.00 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 3DNL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AIK HIV GP41 CORE STRUCTURE Deposited 1997-04-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain C 623–656（34 aa） Fragment：PROTEASE-RESISTANT CORE
Chain N 544–579（36 aa） Fragment：PROTEASE-RESISTANT CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；A 10 MG/ML STOCK WAS DILUTED 1:1 IN A SITTING DROP WITH 80 MM NH4CL, 20% PEG200, AND 50% ISOPROPANOL, AND THEN ALLOWED TO EQUILIBRATE AGAINST 80 MM NH4CL, 20% PEG200, AND 30% ISOPROPANOL., pH 6.0, vapor diffusion - sitting drop
Resolution 2.00 Å R-free 0.266
1DF4 INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION Deposited 1999-11-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 546–579（34 aa） Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)
Chain A 628–655（28 aa） Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；SODIUM CITRATE, AMMONIUM DIHYDROGEN PHOSPHATE, BETA-OG, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.45 Å R-free 0.245
1DF5 INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION Deposited 1999-11-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 546–579（34 aa） Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG-GLY-GLY)
Chain A 628–655（28 aa） Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG-GLY-GLY)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Potassium sodium tartrate, SDS, sodium hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.315
1DLB HELICAL INTERACTIONS IN THE HIV-1 GP41 CORE REVEALS STRUCTURAL BASIS FOR THE INHIBITORY ACTIVITY OF GP41 PEPTIDES Deposited 1999-12-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 546–579（34 aa） Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)
Chain A 628–655（28 aa） Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)
Mutation：Q65L Mutation：Q65L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG 4000, AMMONIUM SULPHATE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.00 Å R-free 0.243
1G9M HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B Deposited 2000-11-24 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 × 4 PDB declaration: tetrameric
Chain G 83–127（45 aa） Fragment：CORE
Chain G 195–297（103 aa） Fragment：CORE
Chain G 330–492（163 aa） Fragment：CORE
Mutation：VARIABLE LOOPS SUBSTITUTED Mutation：VARIABLE LOOPS SUBSTITUTED Mutation：VARIABLE LOOPS SUBSTITUTED NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.330
1GC1 HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY Deposited 1998-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 83–127（45 aa） Fragment：CORE
Chain G 195–297（103 aa） Fragment：CORE
Chain G 330–492（163 aa） Fragment：CORE
Mutation：(GARS) SUBSTITUTION AT THE N TERMINUS, GLY ALA GLY SUBSTITUTIONS FOR THE V1/V2 AND V3 LOOPS Mutation：(GARS) SUBSTITUTION AT THE N TERMINUS, GLY ALA GLY SUBSTITUTIONS FOR THE V1/V2 AND V3 LOOPS Mutation：(GARS) SUBSTITUTION AT THE N TERMINUS, GLY ALA GLY SUBSTITUTIONS FOR THE V1/V2 AND V3 LOOPS NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, vapor diffusion
Resolution 2.50 Å R-free 0.302
1GZL Crystal structure of C14linkmid/IQN17: a cross-linked inhibitor of HIV-1 entry bound to the gp41 hydrophobic pocket Deposited 2002-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 565–581（17 aa） Fragment：GP41 HYDROPHOBIC POCKET, RESIDUES 565-581, GCN4, RESIDUES 249-276
Chain C 628–639（12 aa） Fragment：RESIDUES 628-639
Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES CL CHLORIDE ION × 3 N2P PENTANE-1,5-DIAMINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.6；16% ISOPROPANOL, 0.1 M TRIS, PH 8.6, 1 M (NH4)2SO4
Resolution 1.80 Å R-free 0.243
1GZL Crystal structure of C14linkmid/IQN17: a cross-linked inhibitor of HIV-1 entry bound to the gp41 hydrophobic pocket Deposited 2002-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 565–581（17 aa） Fragment：GP41 HYDROPHOBIC POCKET, RESIDUES 565-581, GCN4, RESIDUES 249-276
Chain D 628–639（12 aa） Fragment：RESIDUES 628-639
Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES CL CHLORIDE ION × 3 N2P PENTANE-1,5-DIAMINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.6；16% ISOPROPANOL, 0.1 M TRIS, PH 8.6, 1 M (NH4)2SO4
Resolution 1.80 Å R-free 0.243
1K33 Crystal structure analysis of the gp41 core mutant Deposited 2001-10-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 546–579（34 aa） Fragment：gp41 ectodomain core
Chain A 628–655（28 aa） Fragment：gp41 ectodomain core
Mutation：I48A Mutation：I48A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 1.75 Å R-free 0.226
1K34 Crystal structure analysis of gp41 core mutant Deposited 2001-10-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 546–579（34 aa） Fragment：gp41 ectodomain core
Chain A 628–655（28 aa） Fragment：gp41 ectodomain core
Mutation：I55A Mutation：I55A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 1.88 Å R-free 0.216
1MZI Solution ensemble structures of HIV-1 gp41 2F5 mAb epitope Deposited 2002-10-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 659–671（13 aa） Fragment：13 residues 2F5 epitope
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；278 K；Ionic strength (raw mmCIF value) 50mM phosphate buffer；Pressure ambient
NMR sample composition 1.5mM peptide, 50mM phosphate buffer, pH 6.5 | 95% H2O/5% D2O
NMR sample composition 1.5mM peptide, 50mM phosphate buffer, pH 6.5 | 100% D2O
Resolution not provided
1RZJ HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B Deposited 2003-12-24 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 × 4 PDB declaration: tetrameric
Chain G 195–492（298 aa） Fragment：CORE
Mutation：VARIABLE LOOPS SUBSTITUTED NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.323
2CMR Crystal structure of the HIV-1 neutralizing antibody D5 Fab bound to the gp41 inner-core mimetic 5-helix Deposited 2006-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 543–582（40 aa） Fragment：5-HELIX, RESIDUES 543-582 AND 625-662
Chain A 625–662（38 aa） Fragment：5-HELIX, RESIDUES 543-582 AND 625-662
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；18% (W/V) PEG 4000, 0.2 M TRI-SODIUM CITRATE DIHYDRATE, 0.1 M TRIS-HCL / PH = 8.5
Resolution 2.00 Å R-free 0.258
2ME1 HIV-1 gp41 clade B double alanine mutant Membrane Proximal External Region peptide in DPC micelle Deposited 2013-09-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 657–683（27 aa） Fragment：membrane proximal external region (UNP residues 657-683)
Mutation：N671A/N674A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；308 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] MPER-HXB2-AA, 100 mM [U-100% 2H] DPC, 20 mg/mL DNA nanotube, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MG1 NMR assignment and structure of a peptide derived from the trans-membrane region of HIV-1 gp41 in the presence of hexafluoroisopropanol Deposited 2013-10-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 683–704（22 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 2；Pressure ambient
NMR sample composition 0.5 mM TMDp, 67.5 % H2O, 7.5 % [U-100% 2H] D2O, 25 % hexafluoroisopropanol, 2 mM HEPES, 0.1 mM DSS, hexafluoroisopropanol/water | hexafluoroisopropanol/water
Resolution not provided
2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 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 G 176–492（317 aa） Fragment：CORE
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.255
2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 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 × 6 PDB declaration: hexameric
Chain G 176–492（317 aa） Fragment：CORE
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.255
2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 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 × 6 PDB declaration: hexameric
Chain G 176–492（317 aa） Fragment：CORE
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.255
2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 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 × 6 PDB declaration: hexameric
Chain G 176–492（317 aa） Fragment：CORE
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.255
2NY7 HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12 Deposited 2006-11-20 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 × 6 PDB declaration: hexameric
Chain G 176–492（317 aa） Fragment：CORE
Mutation：M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å R-free 0.255
2PV6 HIV-1 gp41 Membrane Proximal Ectodomain Region peptide in DPC micelle Deposited 2007-05-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 662–683（22 aa） Fragment：residues 662-683
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；308 K；Ionic strength (raw mmCIF value) no salt；Pressure ambient
NMR sample composition 1mM U-15N,13C MPER + 100mM d38 DPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM U-15N MPER + 100mM d38 DPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM unlabeled MPER + 100mM d38 DPC, 100% D2O | 100% D2O
Resolution not provided
2X7R Crystal structure of a late fusion intermediate of HIV-1 gp41 Deposited 2010-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 629–683（55 aa） Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 629-683
Chain N 528–581（54 aa） Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 534-581
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.1M CITRIC ACID PH 6, 60% MPD
Resolution 2.00 Å R-free 0.214
2X7R Crystal structure of a late fusion intermediate of HIV-1 gp41 Deposited 2010-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 528–581（54 aa） Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 534-581
Chain E 629–683（55 aa） Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 629-683
Not recorded NA SODIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.1M CITRIC ACID PH 6, 60% MPD
Resolution 2.00 Å R-free 0.214
2X7R Crystal structure of a late fusion intermediate of HIV-1 gp41 Deposited 2010-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 528–581（54 aa） Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 534-581
Chain B 629–683（55 aa） Fragment：EXTRA CELLULAR DOMAIN, RESIDUES 629-683
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.1M CITRIC ACID PH 6, 60% MPD
Resolution 2.00 Å R-free 0.214
2XRA crystal structure of the HK20 Fab in complex with a gp41 mimetic 5- Helix Deposited 2010-09-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 543–582（40 aa） Fragment：5-HELIX INNER-CORE MIMETIC COMPRISED OF REPEATS OF RESIDUES 543-582 AND 625-662
Chain A 625–662（38 aa） Fragment：5-HELIX INNER-CORE MIMETIC COMPRISED OF REPEATS OF RESIDUES 543-582 AND 625-662
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 0.2 M AMMONIUM SULPHATE, 25% PEG 3350 (W/V)
Resolution 2.30 Å R-free 0.279
2ZZO Crystal structure of the complex between GP41 fragment N36 and fusion inhibitor C34/S138A Deposited 2009-02-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain C 628–661（34 aa） Fragment：FUSION INHIBITOR PEPTIDE C34, UNP residues 628-661
Chain N 546–581（36 aa） Fragment：GP41 FRAGMENT N36, UNP residues 546-581
Mutation：S138A Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；293 K；100MM SODIUM ACETATE BUFFER, PH4.0, 400MM MAGNESIUM CHLORIDE, 12% ETHANOL, pH 4.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.20 Å R-free 0.283
3DNN Molecular structure for the HIV-1 gp120 trimer in the unliganded state Deposited 2008-07-02 Parsed fields agree Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric
Chain A 90–124（35 aa） Fragment：Core: Residues 90-124
Chain B 198–297（100 aa） Fragment：Core: Residues 198-396
Chain B 330–396（67 aa） Fragment：Core: Residues 198-396
Chain C 410–492（83 aa） Fragment：Core: Residues 410-492
Chain D 90–124（35 aa） Fragment：Core: Residues 90-124
Chain E 198–297（100 aa） Fragment：Core: Residues 198-396
Chain E 330–396（67 aa） Fragment：Core: Residues 198-396
Chain F 410–492（83 aa） Fragment：Core: Residues 410-492
Chain G 90–124（35 aa） Fragment：Core: Residues 90-124
Chain H 198–297（100 aa） Fragment：Core: Residues 198-396
Chain H 330–396（67 aa） Fragment：Core: Residues 198-396
Chain I 410–492（83 aa） Fragment：Core: Residues 410-492
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA；pH 7.2；0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE；Ethane 77K 100%RH Vitrobot
Resolution 20.00 Å
3DNO Molecular structure for the HIV-1 gp120 trimer in the CD4-bound state Deposited 2008-07-02 Parsed fields agree Assembly 1 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric
Chain A 90–124（35 aa） Fragment：Core: Residues 90-124
Chain B 198–297（100 aa） Fragment：Core: Residues 198-396
Chain B 330–396（67 aa） Fragment：Core: Residues 198-396
Chain C 410–492（83 aa） Fragment：Core: Residues 410-492
Chain D 90–124（35 aa） Fragment：Core: Residues 90-124
Chain E 198–297（100 aa） Fragment：Core: Residues 198-396
Chain E 330–396（67 aa） Fragment：Core: Residues 198-396
Chain F 410–492（83 aa） Fragment：Core: Residues 410-492
Chain G 90–124（35 aa） Fragment：Core: Residues 90-124
Chain H 198–297（100 aa） Fragment：Core: Residues 198-396
Chain H 330–396（67 aa） Fragment：Core: Residues 198-396
Chain I 410–492（83 aa） Fragment：Core: Residues 410-492
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA；pH 7.2；0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE；Ethane 77K 100%RH Vitrobot
Resolution 20.00 Å
3J70 Model of gp120, including variable regions, in complex with CD4 and 17b Deposited 2014-04-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain D 31–500（470 aa） Fragment：UNP residues 31-500
Chain P 31–500（470 aa） Fragment：UNP residues 31-500
Chain U 31–500（470 aa） Fragment：UNP residues 31-500
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
3TYG Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with a glycosylated engineered gp120 outer domain with miniV3 (eODmV3) Deposited 2011-09-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 412–419（8 aa）
Chain A 445–477（33 aa）
Chain A 254–297（44 aa）
Chain A 330–401（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；24% PEG 3350, 0.29M CaCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.25 Å R-free 0.257
5C0R Crystal Structure of a Generation 3 Influenza Hemagglutinin Stabilized Stem Complexed with the Broadly Neutralizing Antibody C179 Deposited 2015-06-12 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 × 9 PDB declaration: nonameric
Chain A 628–654（27 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Chain A 546–577（32 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；15% (w/v) PEG 1500, 5% (v/v) MPD, 200 mM ammonium chloride, 100 mM Tris, pH 8.5
Resolution 3.19 Å R-free 0.251
5C0S Crystal structure of a generation 4 influenza hemagglutinin stabilized stem in complex with the broadly neutralizing antibody CR6261 Deposited 2015-06-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 628–654（27 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Chain A 546–577（32 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7% (w/v) PEG 4000, 4.5% (v/v) isopropanol, 100 mM imidazole, pH 6.5
Resolution 4.30 Å R-free 0.310
5HM1 Llama VHH 2E7 in complex with gp41 Deposited 2016-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 582–596（15 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Hepes pH 7.0 30% PEG 6000
Resolution 2.96 Å R-free 0.249
5HM1 Llama VHH 2E7 in complex with gp41 Deposited 2016-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 582–596（15 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Hepes pH 7.0 30% PEG 6000
Resolution 2.96 Å R-free 0.249
5HM1 Llama VHH 2E7 in complex with gp41 Deposited 2016-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 582–596（15 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Hepes pH 7.0 30% PEG 6000
Resolution 2.96 Å R-free 0.249
5KA5 HIV-1 gp41 variant V549E resistance mutation Deposited 2016-06-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 543–582（40 aa） Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain A 625–661（37 aa） Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Mutation：V549E Mutation：V549E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；3M Sodium chloride, 0.1M Sodium Acetate Sample concentration: 6 mg/ml
Resolution 1.80 Å R-free 0.223
5KA6 HIV-1 gp41 variant Q552R and L555M resistance mutations Deposited 2016-06-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 543–582（40 aa） Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain A 625–661（37 aa） Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain B 543–582（40 aa） Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain B 625–661（37 aa） Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain C 543–582（40 aa） Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Chain C 625–661（37 aa） Fragment：UNP residues 543-582 and 625-661 linked via GGRGG
Mutation：Q552R, L555M Mutation：Q552R, L555M Mutation：Q552R, L555M Mutation：Q552R, L555M Mutation：Q552R, L555M Mutation：Q552R, L555M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.3M Calcium Acetate, 0.1M Sodium Cacodylate Sample concentration: 6.35 mg/ml
Resolution 1.85 Å R-free 0.278
6DLN Oligomeric Structure of the HIV gp41 MPER-TMD in Phospholipid Bilayers Deposited 2018-06-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 665–703（39 aa） Fragment：residues 665-703
Chain B 665–703（39 aa） Fragment：residues 665-703
Chain C 665–703（39 aa） Fragment：residues 665-703
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 7.5；263 K；Pressure 1
NMR measurement conditions pH 7.5；233 K；Pressure 1
NMR sample composition 33 % w/w 4-19F-F699 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5 | 10 mM HEPES buffer pH 7.5
NMR sample composition 33 % w/w [U-13C; U-15N]-L684,I686, G694, 19F-5F-W678, 19F-4F-F699 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5 | 10 mM HEPES buffer pH 7.5
NMR sample composition 33 % w/w [U-13C; U-15N]-L669,I686, A700, 13C'-G694, 19F-5F-W680 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5 | 10 mM HEPES buffer pH 7.5
Resolution not provided
6PSA PIE12 D-PEPTIDE AGAINST HIV ENTRY (IN COMPLEX WITH IQN17 Q577R RESISTANCE MUTANT) Deposited 2019-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 565–581（17 aa） Fragment：GP41 HYDROPHOBIC POCKET, RESIDUES 565-581, GCN4, RESIDUES 249-276
Mutation：Q577R Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；294 K；HAMPTON RESEARCH SALT RX SCREEN, CONDITION B4 - 1.8M AMMONIUM CITRATE DIBASIC, 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.6
Resolution 1.30 Å R-free 0.217
8TQ7 Crystal structure of Fab.34.2.12 in complex with MHC-I (H2-Dd) Deposited 2023-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain E 311–320（10 aa） Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
Chain P 311–320（10 aa） Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
Not recorded EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；12% PEG8000, 0.1 M MES, pH 6.5
Resolution 2.80 Å R-free 0.271
8TQ8 Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd) Deposited 2023-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 311–320（10 aa） Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
Not recorded GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；18% PEG4000, 0.1 M MES, pH 6.0, 0.12 M calcium acetate
Resolution 2.69 Å R-free 0.242
8TQ8 Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd) Deposited 2023-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 311–320（10 aa） Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
Not recorded GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；18% PEG4000, 0.1 M MES, pH 6.0, 0.12 M calcium acetate
Resolution 2.69 Å R-free 0.242
8TQ9 Crystal structure of Fab.S19.8 in complex with MHC-I (H2-Dd) Deposited 2023-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 311–320（10 aa） Fragment：HV1: HIV-1 P18-I10 (UNP residues 311-320)
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, 1.0 M lithium sulfate
Resolution 2.90 Å R-free 0.240
8W2Y Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 542–591（50 aa）
Not recorded GOL GLYCEROL × 3 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.4；293 K；0.1M lithium sulfate, 0.1M sodium citrate trihydrate at pH 6.4 and 25% PEG-1500
Resolution 1.63 Å R-free 0.291
8W32 Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 542–591（50 aa）
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.4；293 K；0.1M lithium sulfate, 0.1M sodium citrate trihydrate at pH 6.4 and 25% PEG-1500
Resolution 1.72 Å R-free 0.290
8W37 Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 542–591（50 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.4；293 K；0.1M lithium sulfate, 0.1M sodium citrate trihydrate at pH 6.4 and 25% PEG-1500
Resolution 2.07 Å R-free 0.268
9ARN Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 542–591（50 aa） Fragment：residues 542-591 (Uniprot numbering), plus N-terminal extension
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.4；293 K；0.1M lithium sulfate, 0.1M sodium citrate trihydrate at pH 6.4 and 25% PEG-1500
Resolution 1.41 Å R-free 0.291
9ARP Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 542–591（50 aa） Fragment：residues 542-591 (Uniprot numbering), with N-terminal extension
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；200mM ammonium sulfate, 100mM sodium acetate, 25% w/v PEG 4000 at pH 4.6
Resolution 2.04 Å R-free 0.369
9ARP Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal molecular determinants of antiviral activity Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 542–591（50 aa） Fragment：residues 542-591 (Uniprot numbering), with N-terminal extension
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；200mM ammonium sulfate, 100mM sodium acetate, 25% w/v PEG 4000 at pH 4.6
Resolution 2.04 Å R-free 0.369

38 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENV_HV1H2
Isoform —
PDB entities 1, 2, 3
Chains and sequence ranges Author chain A； PDBConstruct 1–35； UniProt 90–124 Author chain D； PDBConstruct 1–35； UniProt 90–124 Author chain G； PDBConstruct 1–35； UniProt 90–124 Author chain B； PDBConstruct 1–100； UniProt 198–297 Author chain B； PDBConstruct 104–170； UniProt 330–396 Author chain E； PDBConstruct 1–100； UniProt 198–297 Author chain E； PDBConstruct 104–170； UniProt 330–396 Author chain H； PDBConstruct 1–100； UniProt 198–297 Author chain H； PDBConstruct 104–170； UniProt 330–396 Author chain C； PDBConstruct 1–83； UniProt 410–492 Author chain F； PDBConstruct 1–83； UniProt 410–492 Author chain I； PDBConstruct 1–83； UniProt 410–492

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

SAXS scattering curve SAXS Profile

SAXS profile for 3dnl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3dnl
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3dnl
Deposition date deposition_date2008-07-02
Structure title titleMolecular structure for the HIV-1 gp120 trimer in the b12-bound state
Keywords keywords;HIV-1, ENVELOPE GLYCOPROTEIN, IMMUNODEFICIENCY VIRUS, gp120, AIDS, Apoptosis, Cleavage on pair of basic residues, Coiled coil, Envelope protein, Fusion protein, Host-virus interaction, Lipoprotein, Membrane, Palmitate, Viral immunoevasion, Virion, VIRAL PROTEIN ;; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier47.33 Å
Radius of gyration Rg (electron density) rg_electron46.50 Å
Forward intensity I(0) i0141793000.00
Molecular weight molecular_weight96191.0 kDa
Excluded volume excluded_volume119680 ų
Envelope volume envelope_volume184610 ų
Hydration-shell volume shell_volume33755 ų
Envelope diameter envelope_diameter134.8 Å
Shell Rg shell_rg51.21 Å
Envelope Rg envelope_rg43.32 Å
Shape Rg shape_rg46.55 Å
Total Rg total_rg46.56 Å
Total atoms total_atoms6738
Residues n_residues864
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax133.9 Å
Rg (real space) rg_real47.09 Å
Rg uncertainty (real space) rg_real_error1.09 Å
I(0) (real space) i0_real1.4180e+08
I(0) uncertainty (real space) i0_real_error2.7950e+06
Rg (reciprocal space) rg_reciprocal47.33 Å
I(0) (reciprocal space) i0_reciprocal141800000.0000
Solution quality estimate total_estimate0.6712
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary77.1 Å
Skewness Skewness skewness-0.257
Kurtosis Kurtosis kurtosis-1.085
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6598000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.174; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.867; Smooth: 0.331
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▶

8. Citations (1)

▶

9. Files and Curves (10)