SMTL ID : 8yu7.1

Cryo-EM structure of CXCR4 tetramer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

20 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 5 residues within 4Å: Chain A: A.249, C.250, L.289, L.296 Ligands: CLR.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.289, A:L.289, A:L.296 CLR.2: 10 residues within 4Å: Chain A: L.207, I.256, I.260, F.263, I.268, I.269 Chain B: S.45, V.95, V.98, Y.102 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:V.95, B:V.95, B:V.98, B:V.98, A:L.207, A:I.256, A:F.263, A:F.263, A:I.268, A:I.269, A:I.269 Hydrogen bonds: B:Y.102, B:Y.102 CLR.3: 9 residues within 4Å: Chain A: T.50, G.54, L.57, V.58, V.61, P.298, Y.301, A.302 Chain D: L.245 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.50, A:L.57, A:L.57, A:V.58, A:V.61, A:Y.301, D:L.245 CLR.4: 4 residues within 4Å: Chain A: V.81, L.85, W.160, L.164 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.81, A:V.81, A:L.85, A:W.160, A:W.160, A:W.160, A:W.160, A:L.164 CLR.5: 7 residues within 4Å: Chain A: F.35, F.39, F.292 Chain D: K.281, W.282, I.285 Ligands: CLR.18 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:W.282, D:W.282, D:I.285, D:I.285, A:F.35, A:F.39, A:F.292 CLR.6: 10 residues within 4Å: Chain A: S.45, V.95, V.98, Y.102 Chain D: L.207, I.256, I.260, F.263, I.268, I.269 13 PLIP interactions: 7 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:L.207, D:I.256, D:F.263, D:F.263, D:I.268, D:I.269, D:I.269, A:V.95, A:V.95, A:V.98, A:V.98 Hydrogen bonds: A:Y.102, A:Y.102 CLR.7: 7 residues within 4Å: Chain A: K.281, W.282, I.285 Chain B: F.35, F.39, F.292 Ligands: CLR.1 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.35, B:F.39, B:F.292, A:W.282, A:W.282, A:I.285, A:I.285 CLR.8: 5 residues within 4Å: Chain B: A.249, C.250, L.289, L.296 Ligands: CLR.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.289, B:L.289, B:L.296 CLR.9: 10 residues within 4Å: Chain B: L.207, I.256, I.260, F.263, I.268, I.269 Chain C: S.45, V.95, V.98, Y.102 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:L.207, B:I.256, B:F.263, B:F.263, B:I.268, B:I.269, B:I.269, C:V.95, C:V.95, C:V.98, C:V.98 Hydrogen bonds: C:Y.102, C:Y.102 CLR.10: 9 residues within 4Å: Chain A: L.245 Chain B: T.50, G.54, L.57, V.58, V.61, P.298, Y.301, A.302 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.50, B:L.57, B:L.57, B:V.58, B:V.61, B:Y.301, A:L.245 CLR.11: 4 residues within 4Å: Chain B: V.81, L.85, W.160, L.164 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.81, B:V.81, B:L.85, B:W.160, B:W.160, B:W.160, B:W.160, B:L.164 CLR.12: 7 residues within 4Å: Chain B: K.281, W.282, I.285 Chain C: F.35, F.39, F.292 Ligands: CLR.8 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.35, C:F.39, C:F.292, B:W.282, B:W.282, B:I.285, B:I.285 CLR.13: 5 residues within 4Å: Chain C: A.249, C.250, L.289, L.296 Ligands: CLR.16 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.289, C:L.289, C:L.296 CLR.14: 9 residues within 4Å: Chain B: L.245 Chain C: T.50, G.54, L.57, V.58, V.61, P.298, Y.301, A.302 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.50, C:L.57, C:L.57, C:V.58, C:V.61, C:Y.301, B:L.245 CLR.15: 4 residues within 4Å: Chain C: V.81, L.85, W.160, L.164 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.81, C:V.81, C:L.85, C:W.160, C:W.160, C:W.160, C:W.160, C:L.164 CLR.16: 7 residues within 4Å: Chain C: K.281, W.282, I.285 Chain D: F.35, F.39, F.292 Ligands: CLR.13 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.35, D:F.39, D:F.292, C:W.282, C:W.282, C:I.285, C:I.285 CLR.17: 9 residues within 4Å: Chain C: F.263, I.268, I.269 Chain D: S.45, A.94, V.95, V.98, A.99, Y.102 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:F.263, C:F.263, C:I.268, C:I.269, C:I.269, D:A.94, D:V.95, D:V.95, D:V.98, D:V.98, D:A.99 Hydrogen bonds: C:I.268 CLR.18: 5 residues within 4Å: Chain D: A.249, C.250, L.289, L.296 Ligands: CLR.5 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.289, D:L.289, D:L.296 CLR.19: 9 residues within 4Å: Chain C: L.245 Chain D: T.50, G.54, L.57, V.58, V.61, P.298, Y.301, A.302 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:T.50, D:L.57, D:L.57, D:V.58, D:V.61, D:Y.301, C:L.245 CLR.20: 4 residues within 4Å: Chain D: V.81, L.85, W.160, L.164 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.81, D:V.81, D:L.85, D:W.160, D:W.160, D:W.160, D:W.160, D:L.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, A. et al., Structural basis of CXCR4 assembly and regulation. Cell Rep (2025)

Release Date

2025-03-05

Peptides

C-X-C chemokine receptor type 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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C-X-C chemokine receptor type 4