SMTL ID : 9b6e.1

Cryo-EM structure of the mouse TRPM8 channel in complex with the antagonist TC-I 2014

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x T14: 3-{7-(trifluoromethyl)-5-[2-(trifluoromethyl)phenyl]-1H-benzimidazol-2-yl}-1-oxa-2-azaspiro[4.5]dec-2-ene(Non-covalent)

T14.1: 21 residues within 4Å: Chain A: W.799, I.838, L.842, I.845, L.861, M.864, L.865, V.868, F.980 Chain B: L.874, W.878, A.881, F.882, L.960, I.963, Y.964, S.967, L.971, L.972, L.975 Ligands: Y01.5 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.878, B:W.878, B:I.963, A:L.861, A:M.864, A:V.868 Hydrogen bonds: B:W.878, B:S.967 Halogen bonds: B:S.967 T14.6: 21 residues within 4Å: Chain B: W.799, I.838, L.842, I.845, L.861, M.864, L.865, V.868, F.980 Chain C: L.874, W.878, A.881, F.882, L.960, I.963, Y.964, S.967, L.971, L.972, L.975 Ligands: Y01.10 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.878, C:W.878, C:I.963, B:L.861, B:M.864, B:V.868 Hydrogen bonds: C:W.878, C:S.967 Halogen bonds: C:S.967 T14.11: 21 residues within 4Å: Chain C: W.799, I.838, L.842, I.845, L.861, M.864, L.865, V.868, F.980 Chain D: L.874, W.878, A.881, F.882, L.960, I.963, Y.964, S.967, L.971, L.972, L.975 Ligands: Y01.15 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:W.878, D:W.878, D:I.963, C:L.861, C:M.864, C:V.868 Hydrogen bonds: D:W.878, D:S.967 Halogen bonds: D:S.967 T14.16: 21 residues within 4Å: Chain A: L.874, W.878, A.881, F.882, L.960, I.963, Y.964, S.967, L.971, L.972, L.975 Chain D: W.799, I.838, L.842, I.845, L.861, M.864, L.865, V.868, F.980 Ligands: Y01.20 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:W.878, A:W.878, A:I.963, D:L.861, D:M.864, D:V.868 Hydrogen bonds: A:W.878, A:S.967 Halogen bonds: A:S.967

16 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 15 residues within 4Å: Chain A: L.872, M.879, 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 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.958, A:F.901, A:I.905, A:Y.909, A:Y.909 Hydrogen bonds: B:E.954 Salt bridges: A:R.902 Y01.3: 21 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.869, F.873, A.876, V.877, V.880, V.884, F.901, V.904, I.905 Ligands: Y01.4 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.747, A:I.747, A:L.750, A:L.751, A:L.854, B:F.869, B:F.869, B:F.873, B:V.880, B:V.880 Hydrogen bonds: A:S.851, A:N.853 Y01.4: 17 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, A.748, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.697, A:F.736, A:V.743, A:V.744, A:V.744, A:I.747, A:L.751 Hydrogen bonds: A:W.683 Y01.5: 15 residues within 4Å: Chain A: L.798, W.799, M.802, L.835, I.838, I.839, L.842, L.861, Q.862, L.865 Chain B: I.956, P.959, L.960, I.963 Ligands: T14.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.862, B:P.959, B:L.960 Y01.7: 15 residues within 4Å: Chain B: L.872, M.879, 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 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.958, B:F.901, B:I.905, B:Y.909, B:Y.909 Hydrogen bonds: C:E.954 Salt bridges: B:R.902 Y01.8: 21 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.869, F.873, A.876, V.877, V.880, V.884, F.901, V.904, I.905 Ligands: Y01.9 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:I.747, B:I.747, B:L.750, B:L.751, B:L.854, C:F.869, C:F.869, C:F.873, C:V.880, C:V.880 Hydrogen bonds: B:S.851, B:N.853 Y01.9: 17 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, A.748, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.697, B:F.736, B:V.743, B:V.744, B:V.744, B:I.747, B:L.751 Hydrogen bonds: B:W.683 Y01.10: 15 residues within 4Å: Chain B: L.798, W.799, M.802, L.835, I.838, I.839, L.842, L.861, Q.862, L.865 Chain C: I.956, P.959, L.960, I.963 Ligands: T14.6 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Q.862, C:P.959, C:L.960 Y01.12: 15 residues within 4Å: Chain C: L.872, M.879, 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 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.901, C:I.905, C:Y.909, C:Y.909, D:I.958 Salt bridges: C:R.902 Hydrogen bonds: D:E.954 Y01.13: 21 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.869, F.873, A.876, V.877, V.880, V.884, F.901, V.904, I.905 Ligands: Y01.14 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.747, C:I.747, C:L.750, C:L.751, C:L.854, D:F.869, D:F.869, D:F.873, D:V.880, D:V.880 Hydrogen bonds: C:S.851, C:N.853 Y01.14: 17 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, A.748, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.13 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.697, C:F.736, C:V.743, C:V.744, C:V.744, C:I.747, C:L.751 Hydrogen bonds: C:W.683 Y01.15: 15 residues within 4Å: Chain C: L.798, W.799, M.802, L.835, I.838, I.839, L.842, L.861, Q.862, L.865 Chain D: I.956, P.959, L.960, I.963 Ligands: T14.11 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.959, D:L.960, C:Q.862 Y01.17: 15 residues within 4Å: Chain A: E.954, W.955, I.958, P.959, C.962, I.963, L.966 Chain D: L.872, M.879, R.898, F.901, R.902, I.905, Y.906, Y.909 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.901, D:I.905, D:Y.909, D:Y.909 Salt bridges: D:R.902 Hydrogen bonds: A:E.954 Y01.18: 20 residues within 4Å: Chain A: F.869, F.873, A.876, 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 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:F.869, A:F.869, A:F.873, A:V.880, A:V.880, D:I.747, D:I.747, D:L.750, D:L.751, D:L.854 Hydrogen bonds: D:S.851, D:N.853 Y01.19: 17 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, A.748, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.18 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.697, D:F.736, D:V.743, D:V.744, D:V.744, D:I.747, D:L.751 Hydrogen bonds: D:W.683 Y01.20: 15 residues within 4Å: Chain A: I.956, P.959, L.960, I.963 Chain D: L.798, W.799, M.802, L.835, I.838, I.839, L.842, L.861, Q.862, L.865 Ligands: T14.16 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:P.959, A:L.960, D:Q.862

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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