SMTL ID : 9axf.1

Structure of human calcium-sensing receptor in complex with chimeric Gq (miniGisq) protein in detergent

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-1-1-mer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: K.323, N.488, Y.510, N.512, Y.514 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: R.205, N.207, F.539, N.541, D.545 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.488, Y.510, N.512, Y.514 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain B: R.205, N.207, F.539, N.541, D.545 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.205

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 3 residues within 4Å: Chain A: E.257, V.258, N.261 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.257, A:V.258 Hydrogen bonds: A:E.257, A:E.257, A:N.261 NAG.6: 1 residues within 4Å: Chain A: N.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.287 NAG.7: 2 residues within 4Å: Chain A: N.468, Q.476 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.468, A:Q.476 NAG.8: 1 residues within 4Å: Chain A: N.594 No protein-ligand interaction detected (PLIP) NAG.22: 2 residues within 4Å: Chain B: V.258, N.261 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.258 Hydrogen bonds: B:N.261 NAG.23: 3 residues within 4Å: Chain B: N.287, T.289, H.312 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.287 NAG.24: 2 residues within 4Å: Chain B: N.468, Q.476 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.468 NAG.25: 2 residues within 4Å: Chain B: E.593, N.594 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.593

2 x TCR: CYCLOMETHYLTRYPTOPHAN(Non-covalent)

TCR.9: 11 residues within 4Å: Chain A: R.66, W.70, T.145, G.146, S.147, A.168, S.169, S.170, Y.218, E.297, A.298 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.70, A:T.145, A:A.298 Hydrogen bonds: A:S.147, A:A.168, A:S.170, A:E.297 TCR.26: 10 residues within 4Å: Chain B: R.66, W.70, T.145, S.147, A.168, S.169, S.170, Y.218, E.297, A.298 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.70, B:T.145, B:A.298 Hydrogen bonds: B:S.147, B:A.168, B:S.170, B:S.170, B:E.297

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 8 residues within 4Å: Chain A: R.66, R.69, W.70, H.413, L.414, R.415, I.416, S.417 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.70, A:H.413, A:R.415, A:I.416, A:S.417 Salt bridges: A:R.66, A:R.69 PO4.27: 8 residues within 4Å: Chain B: R.66, R.69, W.70, H.413, L.414, R.415, I.416, S.417 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.413, B:H.413, B:R.415, B:I.416, B:S.417 Salt bridges: B:R.66, B:R.69

7 x CA: CALCIUM ION(Non-covalent)

CA.11: 4 residues within 4Å: Chain A: T.100, N.102, A.144, T.145 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.100 CA.12: 3 residues within 4Å: Chain A: R.66, S.302, S.303 No protein-ligand interaction detected (PLIP) CA.13: 2 residues within 4Å: Chain A: G.557, E.558 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.557 CA.28: 5 residues within 4Å: Chain B: I.81, N.82, S.84, L.87, L.88 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:I.81, B:S.84, B:L.87 CA.29: 5 residues within 4Å: Chain B: P.39, T.100, N.102, A.144, T.145 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.100 CA.30: 3 residues within 4Å: Chain B: F.42, P.274, S.302 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.302 CA.31: 1 residues within 4Å: Chain B: G.557 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.557

2 x 9IG: 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine(Non-covalent)

9IG.14: 12 residues within 4Å: Chain A: F.668, Q.681, F.684, G.685, I.777, T.780, W.818, F.821, Y.825, E.837, I.841 Ligands: Y01.18 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.668, A:F.684, A:F.821, A:I.841 Hydrogen bonds: A:Q.681, A:Q.681 pi-Stacking: A:F.684, A:W.818, A:Y.825 9IG.32: 11 residues within 4Å: Chain B: Q.681, F.684, E.767, L.773, I.777, T.780, W.818, F.821, Y.825, E.837, I.841 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.684, B:L.773, B:W.818, B:F.821, B:I.841 Hydrogen bonds: B:Q.681, B:Q.681 pi-Stacking: B:F.684

1 x AV0: Lauryl Maltose Neopentyl Glycol(Non-covalent)

AV0.15: 16 residues within 4Å: Chain A: F.788, F.792, R.795, A.804, K.805, T.808, M.811, F.815 Chain B: F.809, F.854, N.855, Y.858 Ligands: Y01.16, Y01.17, Y01.33, CLR.34 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.788, A:F.792, A:F.815, A:F.815, B:F.854, B:F.854, B:F.854 Hydrogen bonds: A:R.795, A:R.795, B:Y.858

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.16: 13 residues within 4Å: Chain A: L.616, F.619, K.805, L.812, V.817, I.839, F.846, A.850, C.851 Chain B: I.816, S.820 Ligands: AV0.15, CLR.36 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.616, A:F.619, A:L.812, A:V.817, A:I.839, A:F.846, A:A.850, B:I.816 Salt bridges: A:K.805 Y01.17: 7 residues within 4Å: Chain A: F.789, F.792, K.793 Ligands: AV0.15, Y01.18, CLR.20, CLR.34 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.792 Salt bridges: A:K.793, A:K.793 Y01.18: 13 residues within 4Å: Chain A: C.781, A.785, F.788, S.810, F.814, F.815, W.818, I.822, Y.825 Ligands: 9IG.14, Y01.17, CLR.20, CLR.34 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.788, A:F.788, A:F.814, A:F.815, A:W.818, A:I.822, A:Y.825 Y01.33: 15 residues within 4Å: Chain A: M.811, F.815, I.819 Chain B: A.615, L.616, F.619, F.806, F.809, I.813, L.842, A.843, A.850, C.851 Ligands: AV0.15, CLR.34 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.815, A:I.819, B:A.615, B:L.616, B:F.619, B:F.619, B:F.619, B:F.809, B:I.813, B:L.842, B:A.850

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.19: 6 residues within 4Å: Chain A: L.622, L.626, F.846, F.854, Y.858 Ligands: CLR.36 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.622, A:L.626, A:F.846, A:F.854, A:Y.858, A:Y.858 CLR.20: 5 residues within 4Å: Chain A: G.778, C.781, L.782 Ligands: Y01.17, Y01.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.782 CLR.21: 5 residues within 4Å: Chain A: A.628, L.631, G.632, K.636, R.638 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.631, A:K.636 CLR.34: 7 residues within 4Å: Chain A: I.822 Chain B: F.612, F.619 Ligands: AV0.15, Y01.17, Y01.18, Y01.33 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.822, B:F.612, B:F.619 CLR.35: 8 residues within 4Å: Chain B: C.781, A.785, F.788, F.815, I.819, I.822 Ligands: CLR.36, CLR.37 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.785, B:F.788, B:F.815, B:F.815, B:I.819, B:I.819, B:I.822 CLR.36: 5 residues within 4Å: Chain B: F.792, L.812 Ligands: Y01.16, CLR.19, CLR.35 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.792, B:L.812 CLR.37: 7 residues within 4Å: Chain B: L.770, G.774, I.777, G.778, C.781, A.785 Ligands: CLR.35 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.777, B:A.785 CLR.38: 2 residues within 4Å: Chain B: A.628, L.659 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.628, B:L.659

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zuo, H. et al., Promiscuous G-protein activation by the calcium-sensing receptor. Nature (2024)

Release Date

2024-04-17

Peptides

Extracellular calcium-sensing receptor: AB
Guanine nucleotide-binding protein G(i) subunit alpha-1,Adenylate cyclase-stimulating G alpha protein: C
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: D
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: E
Single-chain antibody fragment scFv16: F
Nanobody Nb-35: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
Q

C
A

D
B

E
G

F
H

G
N

Membrane

We predict this structure to be a membrane protein.
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Extracellular calcium-sensing receptor

Guanine nucleotide-binding protein G(i) subunit alpha-1,Adenylate cyclase-stimulating G alpha protein

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

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

Single-chain antibody fragment scFv16

Nanobody Nb-35

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