SMTL ID : 7sk3.1

Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an extracellular Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 10 residues within 4Å: Chain A: K.254, I.255, S.258, V.262, C.266, V.308, V.312, V.315, L.316, I.320 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.312, A:V.315, A:L.316 CLR.2: 10 residues within 4Å: Chain A: L.173, V.177, P.180, S.206, E.209, W.210, G.213, M.214, V.217, L.221 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.180, A:E.209, A:W.210, A:W.210, A:L.221 CLR.3: 10 residues within 4Å: Chain A: V.265, P.269, R.290, T.297, A.298, V.301, T.302, L.305 Ligands: CLR.5, CLR.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.265, A:T.297, A:A.298, A:V.301, A:T.302 CLR.4: 16 residues within 4Å: Chain A: F.135, T.138, C.139, V.142, L.146, Y.150, F.151, R.158, V.162, V.166, L.169, L.173, L.221, V.225, P.226, I.229 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.138, A:V.142, A:V.162 Hydrogen bonds: A:Y.150 CLR.5: 11 residues within 4Å: Chain A: V.44, L.45, T.48, L.49, I.52, I.56, V.301, C.304, L.305, V.308 Ligands: CLR.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.48, A:L.49, A:I.52, A:I.56, A:V.308 CLR.6: 11 residues within 4Å: Chain A: L.268, P.269, V.272, A.273, L.276, L.291, A.294, L.295, A.298, T.302 Ligands: CLR.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.268, A:P.269, A:A.298 CLR.7: 8 residues within 4Å: Chain A: V.68, I.72, L.86, I.90, L.93, W.94, L.97 Ligands: CLR.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.72, A:L.86, A:I.90, A:L.93, A:W.94 CLR.8: 15 residues within 4Å: Chain A: C.83, L.86, N.87, I.90, W.94, L.124, I.125, I.128, N.129, R.164, C.167, I.168, W.171, F.175 Ligands: CLR.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.86, A:I.90, A:I.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yen, Y.C. et al., Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias. Sci Adv (2022)

Release Date

2022-07-27

Peptides

Atypical chemokine receptor 3: A
Stromal cell-derived factor 1: B
CID25 Fab light chain: C
CID25 Fab heavy chain: D
CID24 Fab light chain: E
CID24 Fab heavy chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Atypical chemokine receptor 3

Stromal cell-derived factor 1

CID25 Fab light chain

CID25 Fab heavy chain

CID24 Fab light chain

CID24 Fab heavy chain

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