SMTL ID : 8kh5.1

Cryo-EM structure of the GPR174-Gs complex bound to endogenous lysoPS

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 10 residues within 4Å: Chain A: I.64, I.67, N.68, I.71, L.75, Y.104, L.105, L.143, W.150, C.154 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.71, A:L.75, A:L.105, A:L.143, A:W.150, A:W.150, A:W.150, A:W.150 CLR.3: 10 residues within 4Å: Chain A: Y.111, I.114, Y.115, V.118, C.119, I.145, T.204, P.205, I.208 Ligands: LPS.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.114, A:Y.115, A:Y.115, A:V.118, A:I.145, A:T.204, A:P.205

1 x LPS: O-{HYDROXY[((2R)-2-HYDROXY-3-{[(1S)-1-HYDROXYPENTADECYL]OXY}PROPYL)OXY]PHOSPHORYL}-L-SERINE(Non-covalent)

LPS.2: 26 residues within 4Å: Chain A: Y.30, Y.34, R.83, Y.87, F.103, K.106, Y.107, Y.111, I.153, A.156, L.159, F.160, L.163, R.164, F.177, V.178, M.193, G.197, G.201, F.258, D.261, F.262, K.265, H.282, L.286 Ligands: CLR.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.111, A:I.153, A:L.159, A:F.160, A:F.160, A:F.160, A:L.163, A:F.258, A:F.262 Hydrogen bonds: A:Y.30, A:Y.87, A:Y.107, A:Y.107, A:H.282 Salt bridges: A:R.83, A:K.106, A:R.164, A:R.164, A:K.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nie, Y. et al., Specific binding of GPR174 by endogenous lysophosphatidylserine leads to high constitutive G s signaling. Nat Commun (2023)

Release Date

2023-10-18

Peptides

Probable G-protein coupled receptor 174: A
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short: B
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: C
Nanobody 35: D
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
D

Membrane

We predict this structure to be a membrane protein.
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Probable G-protein coupled receptor 174

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Nanobody 35

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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