SMTL ID : 7sk8.1

Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, an extracellular Fab, and an intracellular Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 12 residues within 4Å: Chain A: C.83, L.86, N.87, I.90, W.94, L.124, I.125, I.128, N.129, I.168, W.171, F.175 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.90 CLR.2: 15 residues within 4Å: Chain A: F.135, T.138, C.139, V.142, L.146, Y.150, F.151, V.162, V.166, L.173, L.221, V.225, P.226, I.229 Ligands: LMN.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.135, A:V.142, A:V.142, A:L.146, A:F.151, A:V.162, A:V.166, A:V.166, A:V.225 CLR.3: 11 residues within 4Å: Chain A: S.252, K.254, I.255, S.258, V.262, V.308, V.312, V.315, L.316, I.320 Ligands: CLR.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.254, A:I.255, A:V.315, A:L.316, A:I.320 CLR.4: 10 residues within 4Å: Chain A: V.265, P.269, H.293, A.294, T.297, A.298, V.301, T.302, L.305 Ligands: CLR.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.294, A:A.298, A:T.302 CLR.5: 13 residues within 4Å: Chain A: V.44, L.45, T.48, L.49, I.52, V.265, C.266, V.301, C.304, L.305, V.308 Ligands: CLR.3, CLR.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.305 CLR.7: 11 residues within 4Å: Chain A: L.173, C.176, V.177, P.180, S.206, E.209, W.210, G.213, M.214, V.217, L.221 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.173, A:V.177, A:W.210

1 x LMN: Lauryl Maltose Neopentyl Glycol(Non-covalent)

LMN.6: 11 residues within 4Å: Chain A: V.142, Y.145, L.146, T.149, Y.150, I.229, V.232, F.233, L.236 Chain F: Y.58 Ligands: CLR.2 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:V.142, A:L.146, A:I.229, A:F.233, F:Y.58 Hydrogen bonds: A:Y.150, F:Y.58

1 x GJ9: (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium(Non-covalent)

GJ9.8: 21 residues within 4Å: Chain A: Y.53, W.102, S.105, L.106, N.110, W.112, H.123, F.126, S.127, L.130, F.131, I.134, D.181, S.218, G.222, W.267, Y.270, H.271, Q.303, S.306, L.307 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.102, A:F.131, A:I.134, A:W.267, A:Y.270, A:L.307, A:L.307 Hydrogen bonds: A:S.105

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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