SMTL ID : 9kuw.1

Cryo-EM structure of dimeric APJR and two Beta-arrestins complex with small molecules

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.49 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 01: (1~{S},2~{S})-~{N}-[4-(2,6-dimethoxyphenyl)-5-(6-methylpyridin-2-yl)-1,2,4-triazol-3-yl]-1-(5-methylpyrimidin-2-yl)-1-oxidanyl-propane-2-sulfonamide

01.1: 15 residues within 4Å: Chain C: F.225, W.232, S.253, I.256, F.257, M.260, R.315, M.330, Y.411, Y.418, M.435, F.438, T.442, S.445, Y.446 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.225, C:I.256, C:Y.411, C:Y.418, C:F.438, C:F.438, C:T.442, C:Y.446 Hydrogen bonds: C:R.315, C:R.315 pi-Stacking: C:W.232, C:Y.418, C:F.438 01.4: 15 residues within 4Å: Chain D: F.225, W.232, S.253, I.256, F.257, M.260, R.315, W.408, Y.411, Y.418, L.434, M.435, F.438, T.442, S.445 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.225, D:I.256, D:W.408, D:Y.411, D:Y.418, D:F.438, D:F.438, D:T.442 Hydrogen bonds: D:R.315 pi-Stacking: D:W.232, D:F.438

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 6 residues within 4Å: Chain C: T.234, R.238, P.243 Chain D: G.245, T.246, F.247 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.247, D:F.247, D:F.247, C:P.243 CLR.3: 6 residues within 4Å: Chain C: T.246, F.247 Chain D: T.234, R.238, P.243, F.244 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:T.234, D:P.243, C:F.247, C:F.247, C:F.247, C:F.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yue, Y. et al., Mechanistic insights into the versatile stoichiometry and biased signaling of the apelin receptor-arrestin complex. Nat Commun (2025)

Release Date

2025-09-17

Peptides

Beta arrestion-scFv30: AB
Apelin receptor: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
Q

D
R

Membrane

We predict this structure to be a membrane protein.
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Beta arrestion-scFv30

Apelin receptor

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