SMTL ID : 9b6i.1

Cryo-EM structure of the avian great tit TRPM8 channel in complex with the antagonist TC-I 2014

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.26 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.793, N.807, D.810 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain B: E.793, N.807, D.810 No protein-ligand interaction detected (PLIP) CA.13: 3 residues within 4Å: Chain C: E.793, N.807, D.810 No protein-ligand interaction detected (PLIP) CA.19: 3 residues within 4Å: Chain D: E.793, N.807, D.810 No protein-ligand interaction detected (PLIP)

16 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 19 residues within 4Å: Chain A: I.757, L.760, L.761, A.764, L.768, Y.843, L.850, F.854, S.857, L.860 Chain B: F.875, F.879, A.882, V.886, V.890, F.907, V.910, I.911 Ligands: Y01.3 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.875, A:I.757, A:I.757, A:L.761, A:A.764, A:L.850 Y01.3: 17 residues within 4Å: Chain A: W.693, N.703, I.707, L.710, F.746, F.749, S.750, V.753, I.754, I.757, A.758, L.761, F.854, V.856, S.857, R.858 Ligands: Y01.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.693, A:I.707, A:F.746, A:I.754, A:I.754, A:F.854 Hydrogen bonds: A:N.703 Y01.4: 14 residues within 4Å: Chain A: L.805, W.806, M.809, L.841, I.844, V.845, L.848, Q.868 Chain B: W.961, I.962, P.965, L.966, I.969 Ligands: T14.5 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.805, A:W.806, A:I.844, A:V.845, A:L.848, B:P.965, B:I.969 Hydrogen bonds: A:Q.868 Y01.6: 16 residues within 4Å: Chain A: L.878, F.881, A.882, M.885, E.904, F.907, R.908, I.911, Y.912, Y.915 Chain B: P.959, E.960, W.961, I.964, P.965, C.968 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.907, A:Y.915, A:Y.915, A:Y.915, B:I.964 Hydrogen bonds: B:P.959 Y01.8: 19 residues within 4Å: Chain B: I.757, L.760, L.761, A.764, L.768, Y.843, L.850, F.854, S.857, L.860 Chain D: F.875, F.879, A.882, V.886, V.890, F.907, V.910, I.911 Ligands: Y01.9 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:I.757, B:I.757, B:L.761, B:A.764, B:L.850, D:F.875 Y01.9: 17 residues within 4Å: Chain B: W.693, N.703, I.707, L.710, F.746, F.749, S.750, V.753, I.754, I.757, A.758, L.761, F.854, V.856, S.857, R.858 Ligands: Y01.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.693, B:I.707, B:F.746, B:I.754, B:I.754, B:F.854 Hydrogen bonds: B:N.703 Y01.10: 14 residues within 4Å: Chain B: L.805, W.806, M.809, L.841, I.844, V.845, L.848, Q.868 Chain D: W.961, I.962, P.965, L.966, I.969 Ligands: T14.11 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:P.965, D:I.969, B:L.805, B:W.806, B:I.844, B:V.845, B:L.848 Hydrogen bonds: B:Q.868 Y01.12: 16 residues within 4Å: Chain B: L.878, F.881, A.882, M.885, E.904, F.907, R.908, I.911, Y.912, Y.915 Chain D: P.959, E.960, W.961, I.964, P.965, C.968 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.907, B:Y.915, B:Y.915, B:Y.915, D:I.964 Hydrogen bonds: D:P.959 Y01.14: 19 residues within 4Å: Chain A: F.875, F.879, A.882, V.886, V.890, F.907, V.910, I.911 Chain C: I.757, L.760, L.761, A.764, L.768, Y.843, L.850, F.854, S.857, L.860 Ligands: Y01.15 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.757, C:I.757, C:L.761, C:A.764, C:L.850, A:F.875 Y01.15: 17 residues within 4Å: Chain C: W.693, N.703, I.707, L.710, F.746, F.749, S.750, V.753, I.754, I.757, A.758, L.761, F.854, V.856, S.857, R.858 Ligands: Y01.14 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.693, C:I.707, C:F.746, C:I.754, C:I.754, C:F.854 Hydrogen bonds: C:N.703 Y01.16: 14 residues within 4Å: Chain A: W.961, I.962, P.965, L.966, I.969 Chain C: L.805, W.806, M.809, L.841, I.844, V.845, L.848, Q.868 Ligands: T14.17 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.805, C:W.806, C:I.844, C:V.845, C:L.848, A:P.965, A:I.969 Hydrogen bonds: C:Q.868 Y01.18: 16 residues within 4Å: Chain A: P.959, E.960, W.961, I.964, P.965, C.968 Chain C: L.878, F.881, A.882, M.885, E.904, F.907, R.908, I.911, Y.912, Y.915 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.964, C:F.907, C:Y.915, C:Y.915, C:Y.915 Hydrogen bonds: A:P.959 Y01.20: 19 residues within 4Å: Chain C: F.875, F.879, A.882, V.886, V.890, F.907, V.910, I.911 Chain D: I.757, L.760, L.761, A.764, L.768, Y.843, L.850, F.854, S.857, L.860 Ligands: Y01.21 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.757, D:I.757, D:L.761, D:A.764, D:L.850, C:F.875 Y01.21: 17 residues within 4Å: Chain D: W.693, N.703, I.707, L.710, F.746, F.749, S.750, V.753, I.754, I.757, A.758, L.761, F.854, V.856, S.857, R.858 Ligands: Y01.20 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.693, D:I.707, D:F.746, D:I.754, D:I.754, D:F.854 Hydrogen bonds: D:N.703 Y01.22: 14 residues within 4Å: Chain C: W.961, I.962, P.965, L.966, I.969 Chain D: L.805, W.806, M.809, L.841, I.844, V.845, L.848, Q.868 Ligands: T14.23 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:P.965, C:I.969, D:L.805, D:W.806, D:I.844, D:V.845, D:L.848 Hydrogen bonds: D:Q.868 Y01.24: 16 residues within 4Å: Chain C: P.959, E.960, W.961, I.964, P.965, C.968 Chain D: L.878, F.881, A.882, M.885, E.904, F.907, R.908, I.911, Y.912, Y.915 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.907, D:Y.915, D:Y.915, D:Y.915, C:I.964 Hydrogen bonds: C:P.959

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)

T14.5: 20 residues within 4Å: Chain A: I.844, L.848, I.851, L.867, M.870, M.871, V.874, F.986 Chain B: L.880, W.884, A.887, F.888, L.966, I.969, Y.970, S.973, L.977, L.978, L.981 Ligands: Y01.4 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.884, B:L.966, B:I.969, A:L.867, A:M.870, A:V.874 Hydrogen bonds: B:W.884 Halogen bonds: B:S.973 T14.11: 20 residues within 4Å: Chain B: I.844, L.848, I.851, L.867, M.870, M.871, V.874, F.986 Chain D: L.880, W.884, A.887, F.888, L.966, I.969, Y.970, S.973, L.977, L.978, L.981 Ligands: Y01.10 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:W.884, D:L.966, D:I.969, B:L.867, B:M.870, B:V.874 Hydrogen bonds: D:W.884 Halogen bonds: D:S.973 T14.17: 20 residues within 4Å: Chain A: L.880, W.884, A.887, F.888, L.966, I.969, Y.970, S.973, L.977, L.978, L.981 Chain C: I.844, L.848, I.851, L.867, M.870, M.871, V.874, F.986 Ligands: Y01.16 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.884, A:L.966, A:I.969, C:L.867, C:M.870, C:V.874 Hydrogen bonds: A:W.884 Halogen bonds: A:S.973 T14.23: 20 residues within 4Å: Chain C: L.880, W.884, A.887, F.888, L.966, I.969, Y.970, S.973, L.977, L.978, L.981 Chain D: I.844, L.848, I.851, L.867, M.870, M.871, V.874, F.986 Ligands: Y01.22 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.884, C:L.966, C:I.969, D:L.867, D:M.870, D:V.874 Hydrogen bonds: C:W.884 Halogen bonds: C:S.973

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
D

D
C

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily M member 8