SMTL ID : 6o77.1

Structure of the TRPM8 cold receptor by single particle electron cryo-microscopy, calcium-bound state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.777, Q.780, N.794, D.797 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.777, A:D.797 CA.5: 4 residues within 4Å: Chain B: E.777, Q.780, N.794, D.797 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.777, B:D.797 CA.9: 4 residues within 4Å: Chain C: E.777, Q.780, N.794, D.797 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.777, C:D.797 CA.13: 4 residues within 4Å: Chain D: E.777, Q.780, N.794, D.797 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.777, D:D.797

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 13 residues within 4Å: Chain A: W.677, I.691, F.730, F.733, S.734, V.737, I.738, I.741, F.841, V.843, S.844, R.845 Ligands: Y01.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.691, A:F.730, A:F.733, A:V.737, A:I.738, A:I.741, A:F.841 Salt bridges: A:R.845 Y01.3: 12 residues within 4Å: Chain A: N.687, W.688, L.744, L.745, Y.830, L.837, F.841, N.846, L.847 Chain D: F.866, V.873 Ligands: Y01.2 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.744, A:L.745, A:L.837, A:F.841, A:L.847, D:F.866, D:V.873 Hydrogen bonds: A:N.846 Y01.4: 12 residues within 4Å: Chain A: M.872, R.889, E.891, F.894, R.895, I.898, Y.899 Chain D: P.946, E.947, W.948, I.951, C.955 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.894, A:I.898, A:Y.899, D:W.948, D:I.951, D:I.951 Salt bridges: A:R.889 Y01.6: 13 residues within 4Å: Chain B: W.677, I.691, F.730, F.733, S.734, V.737, I.738, I.741, F.841, V.843, S.844, R.845 Ligands: Y01.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.691, B:F.730, B:F.733, B:V.737, B:I.738, B:I.741, B:F.841 Salt bridges: B:R.845 Y01.7: 12 residues within 4Å: Chain A: F.866, V.873 Chain B: N.687, W.688, L.744, L.745, Y.830, L.837, F.841, N.846, L.847 Ligands: Y01.6 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.866, A:V.873, B:L.744, B:L.745, B:L.837, B:F.841, B:L.847 Hydrogen bonds: B:N.846 Y01.8: 12 residues within 4Å: Chain A: P.946, E.947, W.948, I.951, C.955 Chain B: M.872, R.889, E.891, F.894, R.895, I.898, Y.899 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.948, A:I.951, A:I.951, B:F.894, B:I.898, B:Y.899 Salt bridges: B:R.889 Y01.10: 13 residues within 4Å: Chain C: W.677, I.691, F.730, F.733, S.734, V.737, I.738, I.741, F.841, V.843, S.844, R.845 Ligands: Y01.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.691, C:F.730, C:F.733, C:V.737, C:I.738, C:I.741, C:F.841 Salt bridges: C:R.845 Y01.11: 12 residues within 4Å: Chain B: F.866, V.873 Chain C: N.687, W.688, L.744, L.745, Y.830, L.837, F.841, N.846, L.847 Ligands: Y01.10 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:F.866, B:V.873, C:L.744, C:L.745, C:L.837, C:F.841, C:L.847 Hydrogen bonds: C:N.846 Y01.12: 12 residues within 4Å: Chain B: P.946, E.947, W.948, I.951, C.955 Chain C: M.872, R.889, E.891, F.894, R.895, I.898, Y.899 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:W.948, B:I.951, B:I.951, C:F.894, C:I.898, C:Y.899 Salt bridges: C:R.889 Y01.14: 13 residues within 4Å: Chain D: W.677, I.691, F.730, F.733, S.734, V.737, I.738, I.741, F.841, V.843, S.844, R.845 Ligands: Y01.15 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.691, D:F.730, D:F.733, D:V.737, D:I.738, D:I.741, D:F.841 Salt bridges: D:R.845 Y01.15: 12 residues within 4Å: Chain C: F.866, V.873 Chain D: N.687, W.688, L.744, L.745, Y.830, L.837, F.841, N.846, L.847 Ligands: Y01.14 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.744, D:L.745, D:L.837, D:F.841, D:L.847, C:F.866, C:V.873 Hydrogen bonds: D:N.846 Y01.16: 12 residues within 4Å: Chain C: P.946, E.947, W.948, I.951, C.955 Chain D: M.872, R.889, E.891, F.894, R.895, I.898, Y.899 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.894, D:I.898, D:Y.899, C:W.948, C:I.951, C:I.951 Salt bridges: D:R.889

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diver, M.M. et al., Structural insights into TRPM8 inhibition and desensitization. Science (2019)

Release Date

2019-09-18

Peptides

Transient receptor potential cation channel subfamily M member 8: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily M member 8

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