SMTL ID : 8szf.1

Cryo-EM structure of cinacalcet-bound active-state human calcium-sensing receptor CaSR in lipid nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

3 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: 4 residues within 4Å: Chain A: R.197, N.199, F.531, N.533 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.197 NAG-NAG.2: 5 residues within 4Å: Chain A: K.315, N.480, Y.502, N.504, Y.506 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: R.219, N.221, F.553, N.555, D.559 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: H.246, V.250, N.253 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.250 NAG.5: 2 residues within 4Å: Chain A: N.460, Q.468 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.460, A:Q.468 NAG.12: 6 residues within 4Å: Chain B: K.337, E.489, N.502, Y.524, N.526, Y.528 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.528 Hydrogen bonds: B:N.502 NAG.13: 2 residues within 4Å: Chain B: N.482, Q.490 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.482 NAG.18: 4 residues within 4Å: Chain B: H.268, E.271, V.272, N.275 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.271, B:V.272 Hydrogen bonds: B:N.275

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.6: 11 residues within 4Å: Chain A: R.58, W.62, T.137, G.138, S.139, A.160, S.161, S.162, Y.210, E.289, A.290 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.62, A:T.137 Hydrogen bonds: A:S.139, A:A.160, A:S.162, A:S.162, A:E.289, W.6 TRP.14: 10 residues within 4Å: Chain B: R.80, T.159, G.160, S.161, A.182, S.183, S.184, Y.232, E.311, A.312 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:S.161, B:A.182, B:S.184, B:S.184, B:E.311, W.14

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: I.73, S.76, L.79, L.80 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.76, A:L.79, A:L.80 CA.8: 1 residues within 4Å: Chain A: G.549 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.549 CA.9: 2 residues within 4Å: Chain A: D.226 Chain B: G.571 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.226 CA.15: 4 residues within 4Å: Chain B: I.95, N.96, S.98, L.102 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.98, B:L.102

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

PO4.10: 8 residues within 4Å: Chain A: R.58, R.61, W.62, H.405, L.406, R.407, I.408, S.409 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.405, A:R.407, A:I.408, A:S.409 Salt bridges: A:R.58, A:R.61 PO4.16: 8 residues within 4Å: Chain B: R.80, R.83, W.84, H.427, L.428, R.429, I.430, S.431 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.84, B:H.427, B:R.429, B:I.430, B:S.431 Salt bridges: B:R.80, B:R.83

2 x YP4: N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine(Non-covalent)

YP4.11: 7 residues within 4Å: Chain A: Q.673, F.676, L.768, I.769, T.772, W.810, Y.817 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.676, A:F.676, A:I.769, A:T.772, A:W.810, A:Y.817, A:Y.817 Hydrogen bonds: A:Q.673 pi-Stacking: A:F.676, A:W.810 YP4.17: 8 residues within 4Å: Chain B: Q.695, F.698, L.784, L.787, G.788, I.791, T.794, W.832 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.787, B:I.791 Hydrogen bonds: B:Q.695 pi-Stacking: B:F.698, B:F.698, B:W.832 Halogen bonds: B:L.784

1 x SPM: SPERMINE(Non-covalent)

SPM.19: 7 residues within 4Å: Chain A: E.220 Chain B: D.252, F.253, S.254, E.255, N.275, S.276 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.253 Hydrogen bonds: B:S.254, B:S.254, B:E.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, F. et al., Allosteric modulation and G-protein selectivity of the Ca 2+ -sensing receptor. Nature (2024)

Release Date

2024-02-07

Peptides

Extracellular calcium-sensing receptor: A
Extracellular calcium-sensing receptor: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

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

Extracellular calcium-sensing receptor

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