SMTL ID : 7sk5.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

7 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 13 residues within 4Å: Chain A: C.83, L.86, N.87, I.90, W.94, I.125, I.128, N.129, R.164, C.167, I.168, W.171 Ligands: CLR.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.86, A:I.90, A:I.125 Hydrogen bonds: A:R.164 CLR.2: 13 residues within 4Å: Chain A: S.252, K.254, I.255, S.258, V.262, V.265, C.266, V.308, V.312, V.315, L.316, I.320 Ligands: CLR.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.312, A:L.316 CLR.3: 10 residues within 4Å: Chain A: L.173, C.176, V.177, P.180, E.209, W.210, G.213, M.214, V.217, L.221 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.210 CLR.4: 9 residues within 4Å: Chain A: V.265, P.269, A.294, T.297, A.298, V.301, T.302, L.305 Ligands: CLR.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.265, A:A.298 CLR.5: 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.169, L.173, L.221, V.225, P.226, I.229 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.135, A:F.135, A:V.162, A:V.166, A:V.225 CLR.6: 7 residues within 4Å: Chain A: V.68, I.72, K.75, L.86, I.90, W.94 Ligands: CLR.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.72 CLR.7: 8 residues within 4Å: Chain A: Y.145, L.146, Y.150, F.233 Chain B: Y.58, G.59, Y.60, T.61 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.58

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
CID24 Fab heavy chain: B
Stromal cell-derived factor 1: C
CID24 Fab light chain: D
Anti-Fab nanobody: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

C
B

D
E

E
K

Membrane

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

CID24 Fab heavy chain

Stromal cell-derived factor 1

CID24 Fab light chain

Anti-Fab nanobody

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