SMTL ID : 7shf.1

Cryo-EM structure of GPR158 coupled to the RGS7-Gbeta5 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-mer

Ligands

22 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 7 residues within 4Å: Chain C: R.528, A.531, L.534, L.535, F.538 Ligands: CLR.2, CLR.12 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.528, C:A.531, C:L.534, C:F.538 CLR.2: 5 residues within 4Å: Chain C: M.527, R.528, A.531 Ligands: CLR.1, CLR.3 No protein-ligand interaction detected (PLIP) CLR.3: 7 residues within 4Å: Chain C: Y.439, L.452, I.453, E.456, T.457, F.460 Ligands: CLR.2 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.439, C:E.456, C:T.457, C:F.460, C:F.460 CLR.4: 8 residues within 4Å: Chain C: W.486, I.542, T.545, S.546, C.549 Chain D: R.577 Ligands: CLR.5, CLR.17 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.486, C:I.542 CLR.5: 6 residues within 4Å: Chain C: F.479, I.482, W.486, L.490, F.538 Ligands: CLR.4 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.479, C:F.479, C:I.482, C:W.486, C:W.486, C:L.490, C:F.538 CLR.6: 7 residues within 4Å: Chain C: L.588, L.591, W.592, Y.595 Ligands: CLR.11, CLR.18, PEE.24 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.588, C:L.591 CLR.7: 4 residues within 4Å: Chain C: Y.580, F.632, V.633 Ligands: CLR.11 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.580, C:F.632, C:V.633 CLR.8: 9 residues within 4Å: Chain C: R.601, R.611, A.614, V.615, H.618, N.619, I.622, I.623 Ligands: CLR.9 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:R.611, C:V.615, C:H.618, C:I.622, C:I.623 CLR.9: 9 residues within 4Å: Chain C: Y.612, V.615, N.619, I.623, L.653, V.657, L.661 Ligands: CLR.8, CLR.10 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.612, C:Y.612, C:V.615, C:I.623 CLR.10: 10 residues within 4Å: Chain C: Y.612, H.652, T.656, V.657, G.660, L.661, I.664, P.665, H.669 Ligands: CLR.9 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.656, C:V.657, C:I.664, C:P.665 Hydrogen bonds: C:H.669 CLR.11: 8 residues within 4Å: Chain C: R.577, Y.580, M.581, L.588 Chain D: I.542, S.546 Ligands: CLR.6, CLR.7 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.542, C:Y.580, C:L.588 Hydrogen bonds: C:R.577 CLR.12: 7 residues within 4Å: Chain C: L.535 Chain D: L.588, W.592, Y.595 Ligands: CLR.1, CLR.17, EIJ.23 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.588, D:Y.595, D:Y.595, C:L.535 CLR.13: 6 residues within 4Å: Chain D: R.611, V.615, H.618, N.619, I.622 Ligands: CLR.14 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.615, D:I.622 CLR.14: 8 residues within 4Å: Chain D: R.611, Y.612, V.615, N.619, I.623, L.661 Ligands: CLR.13, CLR.15 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.612, D:V.615, D:V.615, D:I.623, D:L.661 CLR.15: 9 residues within 4Å: Chain D: Y.612, H.652, T.656, V.657, G.660, L.661, I.664, H.669 Ligands: CLR.14 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.612, D:T.656, D:V.657, D:L.661, D:L.661, D:I.664 Hydrogen bonds: D:H.669 CLR.16: 6 residues within 4Å: Chain D: Y.580, A.583, T.629, F.632, V.633 Ligands: CLR.17 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.632, D:F.632, D:V.633 CLR.17: 10 residues within 4Å: Chain C: W.539, I.542, S.546 Chain D: R.577, Y.580, M.581, L.588 Ligands: CLR.4, CLR.12, CLR.16 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.580, D:L.588, C:I.542, C:I.542 CLR.18: 6 residues within 4Å: Chain D: R.528, A.531, L.534, L.535 Ligands: CLR.6, CLR.19 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:R.528, D:A.531, D:L.535 Hydrogen bonds: D:R.528 CLR.19: 5 residues within 4Å: Chain D: G.523, M.527, R.528 Ligands: CLR.18, CLR.20 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:R.528 CLR.20: 6 residues within 4Å: Chain D: I.453, E.456, T.457, F.460, L.490 Ligands: CLR.19 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.453 CLR.21: 6 residues within 4Å: Chain D: F.479, I.482, L.483, W.486, L.490 Ligands: CLR.22 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.479, D:I.482, D:I.482, D:L.483, D:W.486, D:W.486, D:W.486, D:W.486, D:L.490 CLR.22: 7 residues within 4Å: Chain D: W.486, F.538, I.542, T.545, S.546, C.549 Ligands: CLR.21 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.486, D:W.486, D:F.538, D:I.542, D:I.542

1 x EIJ: (2S)-1-{[(S)-hydroxy{[(1s,2R,3R,4R,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5E,8E,11E,14E)-icosa-5,8,11,14-tetraenoate(Non-covalent)

EIJ.23: 20 residues within 4Å: Chain C: L.489, F.492, R.525, M.529, V.532, I.533, L.535, V.536, W.539, A.585, E.586, F.589 Chain D: L.489, K.508, Y.520, M.529, V.536, W.592 Ligands: CLR.12, PEE.24 16 PLIP interactions: 4 interactions with chain D, 12 interactions with chain C Hydrophobic interactions: D:L.489, D:V.536, C:L.489, C:F.492, C:I.533, C:L.535, C:V.536, C:V.536, C:V.536, C:W.539, C:W.539, C:W.539, C:E.586, C:F.589 Hydrogen bonds: D:K.508 Salt bridges: D:H.504

1 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.24: 17 residues within 4Å: Chain C: M.529, V.536, L.588, W.592 Chain D: L.489, F.492, R.525, M.529, I.533, V.536, V.537, W.539, A.585, E.586, F.589 Ligands: CLR.6, EIJ.23 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.489, D:F.492, D:I.533, D:V.536, D:V.536, D:V.537, D:W.539, D:E.586, D:F.589, C:V.536, C:W.592 Salt bridges: D:R.525

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patil, D.N. et al., Cryo-EM structure of human GPR158 receptor coupled to the RGS7-G beta 5 signaling complex. Science (2022)

Release Date

2021-12-01

Peptides

Isoform 2 of Regulator of G-protein signaling 7: A
Guanine nucleotide-binding protein subunit beta-5: B
G-protein coupled receptor 158: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
B

D
A

Membrane

We predict this structure to be a membrane protein.
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Isoform 2 of Regulator of G-protein signaling 7

Guanine nucleotide-binding protein subunit beta-5

G-protein coupled receptor 158

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