SMTL ID : 9b6d.1

Cryo-EM structure of the mouse TRPM8 channel in the ligand-free desensitized state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

20 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 12 residues within 4Å: Chain A: L.798, W.799, M.802, L.842, I.845, I.858, I.859, L.861, Q.862 Chain B: W.878, I.963 Ligands: Y01.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.799, A:Q.862 Hydrogen bonds: A:Q.862 Y01.2: 18 residues within 4Å: Chain A: I.747, L.750, L.751, A.754, L.758, Y.837, L.844, F.848, S.851, N.853, L.854 Chain B: F.873, V.877, V.880, V.884, F.901, V.904 Ligands: Y01.3 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.747, A:L.751, A:A.754, A:L.844, A:F.848, B:F.873, B:V.884 Hydrogen bonds: A:S.851 Y01.3: 15 residues within 4Å: Chain A: W.683, N.693, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, F.848, V.850, S.851, R.852 Ligands: Y01.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.744, A:F.848 Hydrogen bonds: A:R.852 Y01.4: 15 residues within 4Å: Chain A: L.872, R.898, F.901, R.902, I.905, Y.906, Y.909 Chain B: E.954, W.955, I.958, P.959, C.962, I.963, L.966 Ligands: Y01.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.955, B:I.963, A:F.901, A:Y.909 Hydrogen bonds: B:W.955 Y01.5: 15 residues within 4Å: Chain A: I.845, L.861, L.865, V.868, F.869, L.872 Chain B: L.874, W.878, I.963, L.966, S.967, L.971, L.972 Ligands: Y01.1, Y01.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.963 Hydrogen bonds: B:W.878 Y01.6: 12 residues within 4Å: Chain B: L.798, W.799, M.802, L.842, I.845, I.858, I.859, L.861, Q.862 Chain C: W.878, I.963 Ligands: Y01.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.799, B:Q.862 Hydrogen bonds: B:Q.862 Y01.7: 18 residues within 4Å: Chain B: I.747, L.750, L.751, A.754, L.758, Y.837, L.844, F.848, S.851, N.853, L.854 Chain C: F.873, V.877, V.880, V.884, F.901, V.904 Ligands: Y01.8 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:F.873, C:V.884, B:I.747, B:L.751, B:A.754, B:L.844, B:F.848 Hydrogen bonds: B:S.851 Y01.8: 15 residues within 4Å: Chain B: W.683, N.693, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, F.848, V.850, S.851, R.852 Ligands: Y01.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.744, B:F.848 Hydrogen bonds: B:R.852 Y01.9: 15 residues within 4Å: Chain B: L.872, R.898, F.901, R.902, I.905, Y.906, Y.909 Chain C: E.954, W.955, I.958, P.959, C.962, I.963, L.966 Ligands: Y01.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.901, B:Y.909, C:I.963 Hydrogen bonds: C:W.955 Y01.10: 15 residues within 4Å: Chain B: I.845, L.861, L.865, V.868, F.869, L.872 Chain C: L.874, W.878, I.963, L.966, S.967, L.971, L.972 Ligands: Y01.6, Y01.9 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.963 Hydrogen bonds: C:W.878 Y01.11: 12 residues within 4Å: Chain C: L.798, W.799, M.802, L.842, I.845, I.858, I.859, L.861, Q.862 Chain D: W.878, I.963 Ligands: Y01.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.799, C:Q.862 Hydrogen bonds: C:Q.862 Y01.12: 18 residues within 4Å: Chain C: I.747, L.750, L.751, A.754, L.758, Y.837, L.844, F.848, S.851, N.853, L.854 Chain D: F.873, V.877, V.880, V.884, F.901, V.904 Ligands: Y01.13 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:F.873, D:V.884, C:I.747, C:L.751, C:A.754, C:L.844, C:F.848 Hydrogen bonds: C:S.851 Y01.13: 15 residues within 4Å: Chain C: W.683, N.693, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, F.848, V.850, S.851, R.852 Ligands: Y01.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.744, C:F.848 Hydrogen bonds: C:R.852 Y01.14: 15 residues within 4Å: Chain C: L.872, R.898, F.901, R.902, I.905, Y.906, Y.909 Chain D: E.954, W.955, I.958, P.959, C.962, I.963, L.966 Ligands: Y01.15 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.955, D:I.963, C:F.901, C:Y.909 Y01.15: 15 residues within 4Å: Chain C: I.845, L.861, L.865, V.868, F.869, L.872 Chain D: L.874, W.878, I.963, L.966, S.967, L.971, L.972 Ligands: Y01.11, Y01.14 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.963 Y01.16: 12 residues within 4Å: Chain A: W.878, I.963 Chain D: L.798, W.799, M.802, L.842, I.845, I.858, I.859, L.861, Q.862 Ligands: Y01.20 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.799, D:Q.862 Hydrogen bonds: D:Q.862 Y01.17: 18 residues within 4Å: Chain A: F.873, V.877, V.880, V.884, F.901, V.904 Chain D: I.747, L.750, L.751, A.754, L.758, Y.837, L.844, F.848, S.851, N.853, L.854 Ligands: Y01.18 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:F.873, A:V.884, D:I.747, D:L.751, D:A.754, D:L.844, D:F.848 Hydrogen bonds: D:S.851 Y01.18: 15 residues within 4Å: Chain D: W.683, N.693, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, F.848, V.850, S.851, R.852 Ligands: Y01.17 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.744, D:F.848 Hydrogen bonds: D:R.852 Y01.19: 15 residues within 4Å: Chain A: E.954, W.955, I.958, P.959, C.962, I.963, L.966 Chain D: L.872, R.898, F.901, R.902, I.905, Y.906, Y.909 Ligands: Y01.20 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:F.901, D:Y.909, A:I.963 Hydrogen bonds: A:W.955 Y01.20: 15 residues within 4Å: Chain A: L.874, W.878, I.963, L.966, S.967, L.971, L.972 Chain D: I.845, L.861, L.865, V.868, F.869, L.872 Ligands: Y01.16, Y01.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.963 Hydrogen bonds: A:W.878

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Y. et al., Mechanisms of sensory adaptation and inhibition of the cold and menthol receptor TRPM8. Sci Adv (2024)

Release Date

2024-08-21

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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