SMTL ID : 9b6f.1

Cryo-EM structure of the mouse TRPM8 channel in complex with the antagonist AMG2850

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

16 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 15 residues within 4Å: Chain A: L.798, W.799, M.802, L.835, I.838, I.839, L.842, Q.862, L.865 Chain B: W.878, I.956, P.959, L.960, I.963 Ligands: 01.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.878, B:I.963 Y01.2: 14 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.909 Salt bridges: A:R.898, A:R.898 Y01.3: 18 residues within 4Å: Chain A: I.747, L.750, L.751, A.754, 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, I.905 Ligands: Y01.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.751, A:L.844, B:F.873, B:V.880 Hydrogen bonds: A:N.853 Y01.4: 16 residues within 4Å: Chain A: W.683, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, A.748, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.683, A:I.697, A:F.739, A:V.744, A:F.848 Salt bridges: A:R.852 Y01.6: 15 residues within 4Å: Chain B: L.798, W.799, M.802, L.835, I.838, I.839, L.842, Q.862, L.865 Chain C: W.878, I.956, P.959, L.960, I.963 Ligands: 01.10 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.878, C:I.963 Y01.7: 14 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.909 Salt bridges: B:R.898, B:R.898 Y01.8: 18 residues within 4Å: Chain B: I.747, L.750, L.751, A.754, 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, I.905 Ligands: Y01.9 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.751, B:L.844, C:F.873, C:V.880 Hydrogen bonds: B:N.853 Y01.9: 16 residues within 4Å: Chain B: W.683, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, A.748, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.683, B:I.697, B:F.739, B:V.744, B:F.848 Salt bridges: B:R.852 Y01.11: 15 residues within 4Å: Chain C: L.798, W.799, M.802, L.835, I.838, I.839, L.842, Q.862, L.865 Chain D: W.878, I.956, P.959, L.960, I.963 Ligands: 01.15 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.878, D:I.963 Y01.12: 14 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 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.909 Salt bridges: C:R.898, C:R.898 Y01.13: 18 residues within 4Å: Chain C: I.747, L.750, L.751, A.754, 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, I.905 Ligands: Y01.14 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.873, D:V.880, C:L.751, C:L.844 Hydrogen bonds: C:N.853 Y01.14: 16 residues within 4Å: Chain C: W.683, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, A.748, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.13 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.683, C:I.697, C:F.739, C:V.744, C:F.848 Salt bridges: C:R.852 Y01.16: 15 residues within 4Å: Chain A: W.878, I.956, P.959, L.960, I.963 Chain D: L.798, W.799, M.802, L.835, I.838, I.839, L.842, Q.862, L.865 Ligands: 01.20 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.963 Y01.17: 14 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 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.909 Salt bridges: D:R.898, D:R.898 Y01.18: 18 residues within 4Å: Chain A: F.873, V.877, V.880, V.884, F.901, V.904, I.905 Chain D: I.747, L.750, L.751, A.754, Y.837, L.844, F.848, S.851, N.853, L.854 Ligands: Y01.19 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.751, D:L.844, A:F.873, A:V.880 Hydrogen bonds: D:N.853 Y01.19: 16 residues within 4Å: Chain D: W.683, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, A.748, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.18 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.683, D:I.697, D:F.739, D:V.744, D:F.848 Salt bridges: D:R.852

4 x 01: (8R)-8-[4-(trifluoromethyl)phenyl]-N-[(2S)-1,1,1-trifluoropropan-2-yl]-5,8-dihydro-1,7-naphthyridine-7(6H)-carboxamide

01.5: 17 residues within 4Å: Chain A: W.799, L.842, I.845, L.861, M.864, L.865, V.868, F.980 Chain B: L.874, W.878, I.963, L.966, S.967, L.971, L.972, L.975 Ligands: Y01.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:M.864, B:L.972 Hydrogen bonds: B:W.878 01.10: 17 residues within 4Å: Chain B: W.799, L.842, I.845, L.861, M.864, L.865, V.868, F.980 Chain C: L.874, W.878, I.963, L.966, S.967, L.971, L.972, L.975 Ligands: Y01.6 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.972, B:M.864 Hydrogen bonds: C:W.878 01.15: 17 residues within 4Å: Chain C: W.799, L.842, I.845, L.861, M.864, L.865, V.868, F.980 Chain D: L.874, W.878, I.963, L.966, S.967, L.971, L.972, L.975 Ligands: Y01.11 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.972, C:M.864 Hydrogen bonds: D:W.878 01.20: 17 residues within 4Å: Chain A: L.874, W.878, I.963, L.966, S.967, L.971, L.972, L.975 Chain D: W.799, L.842, I.845, L.861, M.864, L.865, V.868, F.980 Ligands: Y01.16 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:M.864, A:L.972 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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