1df4

INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION

Method: X-RAY DIFFRACTION D_max: 54.1 Å Quality: GOOD

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

HIV-1 ENVELOPE GLYCOPROTEIN GP41

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	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 546–579 Chain A； UniProt 628–655	Fragment：RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)	No other associated polymer	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

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 1DF4	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 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
1DF5 INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION Deposited 1999-11-17	Different construct 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 mutation/modification 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state 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 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
3DNL Molecular structure for the HIV-1 gp120 trimer in the b12-bound state Deposited 2008-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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
3DNN Molecular structure for the HIV-1 gp120 trimer in the unliganded state Deposited 2008-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 method Different experimental conditions Different structure-quality metrics	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 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 oligomeric state Different ligand/ion 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 oligomeric state 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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
Chains and sequence ranges	Author chain A； PDBConstruct 1–34； UniProt 546–579 Author chain A； PDBConstruct 41–68； UniProt 628–655

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	1df4
Deposition date deposition_date	1999-11-17
Structure title title	INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION
Keywords keywords	HIV-1, GP41, MEMBRANE FUSION, PROTEIN-DETERGENT INTERACTION, Viral protein; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	14.72 Å
Radius of gyration Rg (electron density) rg_electron	14.08 Å
Forward intensity I(0) i0	982983.00
Molecular weight molecular_weight	6531.0 kDa
Excluded volume excluded_volume	8168 Å³
Envelope volume envelope_volume	10139 Å³
Hydration-shell volume shell_volume	7028 Å³
Envelope diameter envelope_diameter	51.7 Å
Shell Rg shell_rg	17.71 Å
Envelope Rg envelope_rg	14.53 Å
Shape Rg shape_rg	14.06 Å
Total Rg total_rg	15.04 Å
Total atoms total_atoms	463
Residues n_residues	57
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	54.1 Å
Rg (real space) rg_real	14.86 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	9.8300e+05
I(0) uncertainty (real space) i0_real_error	1.1480e+04
Rg (reciprocal space) rg_reciprocal	14.85 Å
I(0) (reciprocal space) i0_reciprocal	983000.0000
Solution quality estimate total_estimate	0.8206
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.1 Å
Skewness Skewness skewness	0.467
Kurtosis Kurtosis kurtosis	-0.287
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	63920.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.709; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.553; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1df4a_
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.2 — Virus ectodomain
Family Family family	h.3.2.1 — Virus ectodomain

CATH v4.4 (1 domains)

Domain ID domain_id	1df4A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	210 —

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8. Citations (1)

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Unit-cell length a length_a	52.383 Å
Unit-cell length b length_b	52.383 Å
Unit-cell length c length_c	60.982 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	16.500 Å
R factor r_factor	—
R_work r_work	0.2000
R_free r_free	0.2450

Description description	HIV-1 ENVELOPE GLYCOPROTEIN GP41
Molecular weight formula_weight	7879.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	540

INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION

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

HIV-1 ENVELOPE GLYCOPROTEIN GP41

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

fit	/app/data/saxs_computation/df/1df4/1df4.fit
pddf	/app/data/pr_computation/df/1df4/1df4.pr.out
profile	/app/data/saxs_computation/df/1df4/1df4.dat