SMTL ID : 9b6h.1

Cryo-EM structure of the mouse TRPM8 channel in complex with the antagonist TC-I 2014 and the cooling agonist C3

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: 19 residues within 4Å: Chain A: 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 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:M.864, A:V.868, A:F.980, B:W.878, B:W.878, B:A.881, B:I.963 Hydrogen bonds: B:W.878 T14.7: 18 residues within 4Å: Chain B: 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, I.963, Y.964, S.967, L.971, L.972, L.975 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:M.864, B:V.868, B:F.980, C:W.878, C:W.878, C:I.963 Hydrogen bonds: C:W.878 Halogen bonds: C:S.967 T14.13: 19 residues within 4Å: Chain C: 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 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:M.864, C:V.868, C:F.980, D:W.878, D:W.878, D:I.963 Hydrogen bonds: D:W.878 Halogen bonds: D:S.967 T14.19: 19 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: I.838, L.842, I.845, L.861, M.864, L.865, V.868, F.980 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:M.864, D:V.868, D:F.980, A:W.878, A:W.878, A:A.881, A:I.963 Hydrogen bonds: A:W.878

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 13 residues within 4Å: Chain A: 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: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.901, A:Y.909, A:Y.909, B:I.958, B:I.963, B:L.966 Salt bridges: A:R.902 Y01.3: 14 residues within 4Å: Chain A: I.747, L.750, L.751, Y.837, L.844, F.848, S.851, N.853, L.854 Chain B: F.869, F.873, V.880, F.901 Ligands: Y01.4 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.869, B:F.873, A:I.747, A:I.747, A:L.751, A:F.848, A:L.854 Hydrogen bonds: A:S.851, A:N.853 Y01.4: 15 residues within 4Å: Chain A: W.683, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.697, A:V.744, A:L.751 Hydrogen bonds: A:W.683 Y01.8: 12 residues within 4Å: Chain B: R.898, F.901, R.902, I.905, Y.906, Y.909 Chain C: E.954, I.958, P.959, C.962, I.963, L.966 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.901, B:Y.909, B:Y.909, C:I.958, C:L.966 Salt bridges: B:R.902 Y01.9: 16 residues within 4Å: Chain B: I.747, L.750, L.751, Y.837, L.844, F.848, S.851, N.853, L.854 Chain C: F.869, F.873, V.880, V.884, F.901, V.904 Ligands: Y01.10 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:I.747, B:I.747, B:L.751, B:F.848, B:L.854, C:F.869, C:F.873, C:F.873, C:V.880 Hydrogen bonds: B:S.851, B:N.853 Y01.10: 15 residues within 4Å: Chain B: W.683, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.9 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.697, B:V.744, B:L.751 Hydrogen bonds: B:W.683 Y01.14: 13 residues within 4Å: Chain C: 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 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.901, C:Y.909, C:Y.909, D:I.958, D:L.966 Salt bridges: C:R.902 Y01.15: 16 residues within 4Å: Chain C: I.747, L.750, L.751, Y.837, L.844, F.848, S.851, N.853, L.854 Chain D: F.869, F.873, V.880, F.901, V.904, I.905 Ligands: Y01.16 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:F.869, D:F.869, D:F.873, D:F.873, D:V.880, C:I.747, C:I.747, C:L.751, C:F.848, C:L.854 Hydrogen bonds: C:S.851, C:N.853 Y01.16: 15 residues within 4Å: Chain C: W.683, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.15 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.697, C:V.744, C:L.751 Hydrogen bonds: C:W.683 Y01.20: 13 residues within 4Å: Chain A: E.954, W.955, I.958, P.959, C.962, I.963, L.966 Chain D: R.898, F.901, R.902, I.905, Y.906, Y.909 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:W.955, A:I.958, A:P.959, A:I.963, A:L.966, D:F.901, D:Y.909, D:Y.909 Salt bridges: D:R.902 Y01.21: 15 residues within 4Å: Chain A: F.869, F.873, V.880, F.901, V.904 Chain D: I.747, L.750, L.751, Y.837, L.844, F.848, S.851, N.853, L.854 Ligands: Y01.22 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:F.869, A:F.873, A:V.880, D:I.747, D:I.747, D:L.751, D:F.848, D:L.854 Hydrogen bonds: D:S.851, D:N.853 Y01.22: 15 residues within 4Å: Chain D: W.683, I.697, F.701, F.736, F.739, S.740, V.743, V.744, I.747, L.751, F.848, V.850, S.851, R.852 Ligands: Y01.21 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.697, D:V.744, D:L.751 Hydrogen bonds: D:W.683

4 x ULO: nonyl(oxo)di(propan-2-yl)-lambda~5~-phosphane(Non-covalent)

ULO.5: 16 residues within 4Å: Chain A: F.739, N.742, V.743, F.745, Y.746, L.779, M.802, D.803, G.806, L.807, I.839, F.840, R.843, I.847, Y.1006, F.1014 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.742, A:Y.746, A:L.779, A:D.803, A:I.839, A:F.840, A:I.847, A:F.1014 ULO.11: 16 residues within 4Å: Chain B: F.739, N.742, V.743, F.745, Y.746, L.779, M.802, D.803, G.806, L.807, I.839, F.840, R.843, I.847, Y.1006, F.1014 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.742, B:Y.746, B:L.779, B:D.803, B:I.839, B:F.840, B:I.847, B:F.1014 ULO.17: 16 residues within 4Å: Chain C: F.739, N.742, V.743, F.745, Y.746, L.779, M.802, D.803, G.806, L.807, I.839, F.840, R.843, I.847, Y.1006, F.1014 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:N.742, C:Y.746, C:L.779, C:D.803, C:I.839, C:F.840, C:I.847, C:F.1014 ULO.23: 16 residues within 4Å: Chain D: F.739, N.742, V.743, F.745, Y.746, L.779, M.802, D.803, G.806, L.807, I.839, F.840, R.843, I.847, Y.1006, F.1014 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:N.742, D:Y.746, D:L.779, D:D.803, D:I.839, D:F.840, D:I.847, D:F.1014

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.6: 3 residues within 4Å: Chain A: S.933, N.935, E.936 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.935 NAG.12: 3 residues within 4Å: Chain B: S.933, N.935, E.936 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.935 NAG.18: 3 residues within 4Å: Chain C: S.933, N.935, E.936 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.935 NAG.24: 3 residues within 4Å: Chain D: S.933, N.935, E.936 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.935

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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