SMTL ID : 9b6g.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.81 Å

Oligo State

homo-tetramer

Ligands

20 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 16 residues within 4Å: Chain A: L.798, W.799, M.802, I.838, I.839, L.842, I.845, H.846, I.858, I.859, L.861, Q.862 Chain B: W.878, P.959, I.963 Ligands: Y01.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.799, A:L.842, A:I.858 Hydrogen bonds: A:W.799 Y01.2: 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.873, A.876, V.877, V.880, V.884, I.900, F.901, V.904, I.905 Ligands: Y01.3 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.754, A:F.848, A:L.854, B:F.873, B:F.873, B:V.880, B:F.901 Hydrogen bonds: A:N.853 Y01.3: 19 residues within 4Å: Chain A: W.683, Y.684, 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, W.995 Ligands: Y01.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.697, A:V.744, A:V.744, A:L.751, A:F.848 Hydrogen bonds: A:V.850 Salt bridges: A:R.999 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, Y01.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.861, A:V.868, A:L.872, B:I.963, B:L.971 Y01.6: 16 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 Ligands: Y01.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.954, B:W.955, B:I.958, B:I.958, B:I.963, A:F.901 Y01.8: 16 residues within 4Å: Chain B: L.798, W.799, M.802, I.838, I.839, L.842, I.845, H.846, I.858, I.859, L.861, Q.862 Chain C: W.878, P.959, I.963 Ligands: Y01.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.799, B:L.842, B:I.858 Hydrogen bonds: B:W.799 Y01.9: 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.873, A.876, V.877, V.880, V.884, I.900, F.901, V.904, I.905 Ligands: Y01.10 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.754, B:F.848, B:L.854, C:F.873, C:F.873, C:V.880, C:F.901 Hydrogen bonds: B:N.853 Y01.10: 19 residues within 4Å: Chain B: W.683, Y.684, 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, W.995 Ligands: Y01.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.697, B:V.744, B:V.744, B:L.751, B:F.848 Hydrogen bonds: B:V.850 Salt bridges: B:R.999 Y01.12: 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: Y01.8, Y01.13 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.963, C:L.971, B:L.861, B:V.868, B:L.872 Y01.13: 16 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 Ligands: Y01.12 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.901, C:E.954, C:W.955, C:I.958, C:I.963 Y01.15: 16 residues within 4Å: Chain C: L.798, W.799, M.802, I.838, I.839, L.842, I.845, H.846, I.858, I.859, L.861, Q.862 Chain D: W.878, P.959, I.963 Ligands: Y01.19 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.799, C:L.842, C:I.858 Hydrogen bonds: C:W.799 Y01.16: 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.873, A.876, V.877, V.880, V.884, I.900, F.901, V.904, I.905 Ligands: Y01.17 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:A.754, C:F.848, C:L.854, D:F.873, D:F.873, D:V.880, D:F.901 Hydrogen bonds: C:N.853 Y01.17: 19 residues within 4Å: Chain C: W.683, Y.684, 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, W.995 Ligands: Y01.16 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.697, C:V.744, C:V.744, C:L.751, C:F.848 Hydrogen bonds: C:V.850 Salt bridges: C:R.999 Y01.19: 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: Y01.15, Y01.20 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.963, D:L.971, C:L.861, C:V.868, C:L.872 Y01.20: 16 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 Ligands: Y01.19 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:E.954, D:W.955, D:I.958, D:I.963, C:F.901 Y01.22: 16 residues within 4Å: Chain A: W.878, P.959, I.963 Chain D: L.798, W.799, M.802, I.838, I.839, L.842, I.845, H.846, I.858, I.859, L.861, Q.862 Ligands: Y01.26 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.799, D:L.842, D:I.858 Hydrogen bonds: D:W.799 Y01.23: 21 residues within 4Å: Chain A: F.873, A.876, V.877, V.880, V.884, I.900, F.901, V.904, I.905 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: Y01.24 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:A.754, D:F.848, D:L.854, A:F.873, A:F.873, A:V.880, A:F.901 Hydrogen bonds: D:N.853 Y01.24: 19 residues within 4Å: Chain D: W.683, Y.684, 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, W.995 Ligands: Y01.23 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.697, D:V.744, D:V.744, D:L.751, D:F.848 Hydrogen bonds: D:V.850 Salt bridges: D:R.999 Y01.26: 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: Y01.22, Y01.27 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.861, D:V.868, D:L.872, A:I.963, A:L.971 Y01.27: 16 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 Ligands: Y01.26 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:E.954, A:W.955, A:I.958, A:I.963, D:F.901

4 x LQ7: N-(3-aminopropyl)-2-[(3-methylphenyl)methoxy]-N-[(thiophen-2-yl)methyl]benzamide(Non-covalent)

LQ7.4: 22 residues within 4Å: Chain A: F.739, N.742, V.743, Y.746, L.779, D.782, E.783, Q.786, Y.794, N.800, D.803, G.806, L.807, I.839, F.840, R.843, I.847, E.1005, Y.1006, R.1009, F.1014, V.1017 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.742, A:D.803, A:F.840, A:F.1014 Hydrogen bonds: A:Y.794, A:R.843 pi-Cation interactions: A:R.843 LQ7.11: 22 residues within 4Å: Chain B: F.739, N.742, V.743, Y.746, L.779, D.782, E.783, Q.786, Y.794, N.800, D.803, G.806, L.807, I.839, F.840, R.843, I.847, E.1005, Y.1006, R.1009, F.1014, V.1017 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.742, B:D.803, B:F.840, B:F.1014 Hydrogen bonds: B:Y.794, B:R.843 pi-Cation interactions: B:R.843 LQ7.18: 22 residues within 4Å: Chain C: F.739, N.742, V.743, Y.746, L.779, D.782, E.783, Q.786, Y.794, N.800, D.803, G.806, L.807, I.839, F.840, R.843, I.847, E.1005, Y.1006, R.1009, F.1014, V.1017 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:N.742, C:D.803, C:F.840, C:F.1014 Hydrogen bonds: C:Y.794, C:R.843 pi-Cation interactions: C:R.843 LQ7.25: 22 residues within 4Å: Chain D: F.739, N.742, V.743, Y.746, L.779, D.782, E.783, Q.786, Y.794, N.800, D.803, G.806, L.807, I.839, F.840, R.843, I.847, E.1005, Y.1006, R.1009, F.1014, V.1017 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:N.742, D:D.803, D:F.840, D:F.1014 Hydrogen bonds: D:Y.794, D:R.843 pi-Cation interactions: D:R.843

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

NAG.7: 3 residues within 4Å: Chain A: S.933, N.935, E.936 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.933, A:N.935, A:E.936, A:E.936 NAG.14: 3 residues within 4Å: Chain B: S.933, N.935, E.936 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.933, B:N.935, B:E.936, B:E.936 NAG.21: 3 residues within 4Å: Chain C: S.933, N.935, E.936 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.933, C:N.935, C:E.936, C:E.936 NAG.28: 3 residues within 4Å: Chain D: S.933, N.935, E.936 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.933, D:N.935, D:E.936, D:E.936

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.
Show / Hide

Transient receptor potential cation channel subfamily M member 8

Related Entries With Identical Sequence