9men

CryoEM structure of hCXCR4 tetramer bound to HIV-2/gp120/V3 loop

Method: ELECTRON MICROSCOPY D_max: 95.3 Å Quality: GOOD

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

C-X-C chemokine receptor type 4

Homo sapiens

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–352 Chain B； UniProt 1–352 Chain C； UniProt 1–352 Chain D； UniProt 1–352	Not recorded	Surface protein gp120 × 1 （P05883）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.57 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 9MEN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
22XC Structure of CXCR4 in complex with a de-novo designed mini-protein antagonist Deposited 2026-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 2–352（351 aa） Chain G 2–352（351 aa） Chain R 2–352（351 aa）	Not recorded	CLR CHOLESTEROL × 3 D21 (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
2K03 Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21 Deposited 2008-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–38（38 aa） Fragment：N-terminus, residues 1-38 Chain D 1–38（38 aa） Fragment：N-terminus, residues 1-38	Mutation：C28A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C28A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT NMR sample composition .338 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .970 mM CXCR4, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.07 mM [U-100% 13C; U-100% 15N] CXCR4, 0.67 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K04 Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines Deposited 2008-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–38（38 aa） Fragment：N-terminus, residues 1-38 Chain D 1–38（38 aa） Fragment：N-terminus, residues 1-38	Mutation：C28A Mutation：C28A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT NMR sample composition .31 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .775 mM CXCR4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] CXCR4, 0.625 mM CXCL12/SDF1-alpha, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2K05 Structure of SDF1 in complex with the CXCR4 N-terminus containing sulfotyrosines at postitions 7, 12 and 21 Deposited 2008-01-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–38（38 aa） Fragment：N-terminus, residues 1-38 Chain D 1–38（38 aa） Fragment：N-terminus, residues 1-38	Mutation：C28A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C28A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT NMR sample composition .338 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .97 mM CXCR4, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.07 mM [U-100% 13C; U-100% 15N] CXCR4, 0.67 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N55 Structure of constitutively monomeric CXCL12 in complex with the CXCR4 N-terminus Deposited 2015-07-07	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 B 1–38（38 aa）	Mutation：C28A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 2 mM [U-99% 13C; U-99% 15N] protein_1, 25 mM [U-2H] MES, 10 % [U-99% 2H] D2O, 0.02 % sodium azide, 2 mM protein_2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] protein_2, 25 mM [U-2H] MES, 0.02 % sodium azide, 10 % [U-99% 2H] D2O, 2 mM protein_1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3ODU The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t Deposited 2010-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–229（228 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain A 230–319（90 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain B 2–229（228 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain B 230–319（90 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319	Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T	ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 5 OLA OLEIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；Lipidic cubic phase made of monoolein and cholesterol, 20% PEG400, 0.3M Sodium malonate, 5mM Taurine, 0.1M Sodium citrate, pH 5.5, LIPIDIC CUBIC PHASE, temperature 293K	Resolution 2.50 Å R-free 0.282
3OE0 Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide antagonist CVX15 Deposited 2010-08-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–228（227 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319 Chain A 231–319（89 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319	Mutation：L125W, T240P, C1054T, C1097T Mutation：L125W, T240P, C1054T, C1097T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；Lipidic cubic phase made of monoolein and cholesterol, 25% PEG400, 0.3M Potassium sodium tartrate, 0.1 M Tris pH 7.0, LIPIDIC CUBIC PHASE, temperature 293K	Resolution 2.90 Å R-free 0.267
3OE6 Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in I222 spacegroup Deposited 2010-08-12	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 Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–229（228 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-325 Chain A 230–325（96 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-325	Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T	ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；Lipidic cubic phase made of monoolein and cholesterol, 20-26% PEG400, 0.3M Sodium malonate, 5mM Nickel chloride, 0.1M Sodium citrate pH 5.0-5.5, LIPIDIC CUBIC PHASE, temperature 293K	Resolution 3.20 Å R-free 0.306
3OE8 Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in P1 spacegroup Deposited 2010-08-12	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 Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–229（228 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain B 230–319（90 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain C 2–229（228 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain C 230–319（90 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319	Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T	ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K	Resolution 3.10 Å R-free 0.295
3OE8 Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in P1 spacegroup Deposited 2010-08-12	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 Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–229（228 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain A 230–319（90 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain B 2–229（228 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain B 230–319（90 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain C 2–229（228 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain C 230–319（90 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319	Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T	ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 3	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K	Resolution 3.10 Å R-free 0.295
3OE8 Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in P1 spacegroup Deposited 2010-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–229（228 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319 Chain A 230–319（90 aa） Fragment：CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319	Mutation：L125W, C1054T, C1097T Mutation：L125W, C1054T, C1097T	ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K	Resolution 3.10 Å R-free 0.295
3OE9 Crystal structure of the chemokine CXCR4 receptor in complex with a small molecule antagonist IT1t in P1 spacegroup Deposited 2010-08-12	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 Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–228（227 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319 Chain A 231–319（89 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319 Chain B 2–228（227 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319 Chain B 231–319（89 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319	Mutation：L125W, T240P, C1054T, C1097T Mutation：L125W, T240P, C1054T, C1097T Mutation：L125W, T240P, C1054T, C1097T Mutation：L125W, T240P, C1054T, C1097T	ITD (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；Lipidic cubic phase made of monoolein and cholesterol, 27-35% PEG400, 0.27-0.33M Sodium malonate, 5mM Hexamine cobalt chloride, 0.1M MES pH 6.0, LIPIDIC CUBIC PHASE, temperature 293K	Resolution 3.10 Å R-free 0.284
4RWS Crystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI Community Target) Deposited 2014-12-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–228（227 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319 Chain A 231–319（89 aa） Fragment：CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319	Mutation：L125W, T240P, D187C, C1054T, C1097T Mutation：L125W, T240P, D187C, C1054T, C1097T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；100 mM sodium citrate pH 5.5, 28% PEG 400, 120 mM ammonium phosphate dibasic, 2-6% polypropylene P400, Lipidic cubic phase, temperature 293K	Resolution 3.10 Å R-free 0.274
8GP3 Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4 Deposited 2022-08-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain U 336–352（17 aa） Chain V 336–352（17 aa）	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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 3 seconds before plunging.	Resolution 4.80 Å
8I0Q Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4 (Local refine) Deposited 2023-01-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain U 336–352（17 aa） Chain V 336–352（17 aa）	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	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 3 seconds before plunging.	Resolution 4.45 Å
8K3Z Cryo-EM structure of CXCR4 in complex with CXCL12 Deposited 2023-07-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 25–320（296 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
8U4N Structure of Apo CXCR4/Gi complex Deposited 2023-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 2–352（351 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.72 Å
8U4O Structure of CXCL12-bound CXCR4/Gi complex Deposited 2023-09-11	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–352（351 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8U4P Structure of AMD3100-bound CXCR4/Gi complex Deposited 2023-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 2–352（351 aa）	Not recorded	CLR CHOLESTEROL × 1 VH6 Plerixafor × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8U4Q Structure of REGN7663 Fab-bound CXCR4/Gi complex Deposited 2023-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 2–352（351 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å
8U4R Structure of REGN7663-Fab bound CXCR4 Deposited 2023-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 2–352（351 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8U4S Structure of trimeric CXCR4 in complex with REGN7663 Fab Deposited 2023-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 2–352（351 aa） Chain G 2–352（351 aa） Chain R 2–352（351 aa）	Not recorded	CLR CHOLESTEROL × 6 D21 (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
8U4T Structure of tetrameric CXCR4 in complex with REGN7663 Fab Deposited 2023-09-11	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain AA 2–352（351 aa） Chain I 2–352（351 aa） Chain Q 2–352（351 aa） Chain R 2–352（351 aa）	Not recorded	CLR CHOLESTEROL × 16 D21 (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
8YU7 Cryo-EM structure of CXCR4 tetramer Deposited 2024-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–352（351 aa） Chain B 2–352（351 aa） Chain C 2–352（351 aa） Chain D 2–352（351 aa）	Not recorded	CLR CHOLESTEROL × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8ZPL Cryo-EM strucutre of CXCR4 complexed with antagonist HF51116 Deposited 2024-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 1–224（224 aa） Chain R 241–319（79 aa）	Not recorded	CLR CHOLESTEROL × 2 A1D8K (2S)-N-[[4-[[3-(cyclohexylamino)propylamino]methyl]phenyl]methyl]-5-(diaminomethylideneamino)-2-(pyridin-2-ylmethylamino)pentanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8ZPM Cryo-EM strucutre of CXCR4 complexed with antagonist AMD070 Deposited 2024-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 1–224（224 aa） Chain R 241–319（79 aa）	Not recorded	A1D8L Mavorixafor × 1 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8ZPN Cryo-EM strucutre of CXCR4 complexed with antagonist AMD3100 Deposited 2024-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 1–224（224 aa） Chain R 241–319（79 aa）	Not recorded	CLR CHOLESTEROL × 1 VH6 Plerixafor × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
9MDU Human CXCR4 tetramer Deposited 2024-12-05	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9ME1 hCXCR4-CXCL12 complex with 1:1 stoichiometry Deposited 2024-12-05	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa） Chain E 1–352（352 aa） Chain I 1–352（352 aa） Chain K 1–352（352 aa） Chain L 1–352（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
9MEJ Global structure of hCXCR4 and HIV-2 gp120 Deposited 2024-12-06	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.99 Å
9MET CXCR4-HIV-2/gp120-CD4 Deposited 2024-12-08	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain M 1–352（352 aa） Chain N 1–352（352 aa） Chain O 1–352（352 aa） Chain S 1–352（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.65 Å
9MEU CXCR4 tetramer bound to 4 CXCL12 dimers Deposited 2024-12-08	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–352（352 aa） Chain B 1–352（352 aa） Chain C 1–352（352 aa） Chain D 1–352（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
9UPU Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a Deposited 2025-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–337（337 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9UPV Cryo-EM structure of CXCR4 complexed with agonist SDVX1 Deposited 2025-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 1–337（337 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

32 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CXCR4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–352； UniProt 1–352 Author chain B； PDBConstruct 1–352； UniProt 1–352 Author chain C； PDBConstruct 1–352； UniProt 1–352 Author chain D； PDBConstruct 1–352； UniProt 1–352

Surface protein gp120

Virus-associated RNAs

UniProt P05883

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain E； UniProt 300–321	Fragment：V3 loop (UNP residues 300-321)	C-X-C chemokine receptor type 4 × 4 （P61073）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.57 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ENV_HV2NZ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–20； UniProt 300–321

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	9men
Deposition date deposition_date	2024-12-07
Structure title title	CryoEM structure of hCXCR4 tetramer bound to HIV-2/gp120/V3 loop
Keywords keywords	HIV-2 gp120, V3 loop, hCXCR4, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	33.73 Å
Radius of gyration Rg (electron density) rg_electron	32.52 Å
Forward intensity I(0) i0	212082000.00
Molecular weight molecular_weight	131180.0 kDa
Excluded volume excluded_volume	170480 Å³
Envelope volume envelope_volume	225590 Å³
Hydration-shell volume shell_volume	55140 Å³
Envelope diameter envelope_diameter	102.8 Å
Shell Rg shell_rg	41.70 Å
Envelope Rg envelope_rg	31.70 Å
Shape Rg shape_rg	32.50 Å
Total Rg total_rg	33.46 Å
Total atoms total_atoms	9281
Residues n_residues	1144
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	95.3 Å
Rg (real space) rg_real	33.45 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	2.1210e+08
I(0) uncertainty (real space) i0_real_error	3.0440e+06
Rg (reciprocal space) rg_reciprocal	33.63 Å
I(0) (reciprocal space) i0_reciprocal	212100000.0000
Solution quality estimate total_estimate	0.8929
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.6 Å
Skewness Skewness skewness	-0.110
Kurtosis Kurtosis kurtosis	-0.534
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	112000000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.881

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	C-X-C chemokine receptor type 4
Molecular weight formula_weight	40784.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9281

MEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSSDYKDDDDK

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Surface protein gp120
Molecular weight formula_weight	2261.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

NKTVLPIMSGFKFHSKPVIN

来源 Source

来源生物 organism	Virus-associated RNAs
NCBI Class编号 ncbi_taxonomy_id	1425366
宿主生物 host_organism	Homo sapiens

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8. Citations (1)

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

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

Resolution resolution	3.570 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.57 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	117147

fit	/app/data/saxs_computation/me/9men/9men.fit
pddf	/app/data/pr_computation/me/9men/9men.pr.out
profile	/app/data/saxs_computation/me/9men/9men.dat

CryoEM structure of hCXCR4 tetramer bound to HIV-2/gp120/V3 loop

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

C-X-C chemokine receptor type 4

State in the Current Structure

Other States of the Same Protein in the Database

Surface protein gp120

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)