SMTL ID : 8e4m.1

The intermediate C2-state mouse TRPM8 structure in complex with the cooling agonist C3 and PI(4,5)P2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.1: 23 residues within 4Å: Chain A: S.680, Y.684, R.689, N.693, I.697, L.700, F.701, F.736, F.739, S.740, V.743, V.744, I.747, I.847, F.848, V.850, S.851, R.852, N.853, L.854, R.999 Chain D: K.606, F.873 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.701, A:F.736, A:V.743, A:V.744, A:I.747, A:I.847 Hydrogen bonds: A:S.680, A:S.680, A:N.693, A:S.851, A:R.852, A:N.853, A:N.853, D:K.606 Salt bridges: A:R.689, A:R.852, A:R.999, D:K.606, D:K.606 PIO.4: 23 residues within 4Å: Chain A: K.606, F.873 Chain B: S.680, Y.684, R.689, N.693, I.697, L.700, F.701, F.736, F.739, S.740, V.743, V.744, I.747, I.847, F.848, V.850, S.851, R.852, N.853, L.854, R.999 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.701, B:F.736, B:V.743, B:V.744, B:I.747, B:I.847 Hydrogen bonds: B:S.680, B:S.680, B:N.693, B:S.851, B:R.852, B:N.853, B:N.853, A:K.606 Salt bridges: B:R.689, B:R.852, B:R.999, A:K.606, A:K.606 PIO.7: 23 residues within 4Å: Chain B: K.606, F.873 Chain C: S.680, Y.684, R.689, N.693, I.697, L.700, F.701, F.736, F.739, S.740, V.743, V.744, I.747, I.847, F.848, V.850, S.851, R.852, N.853, L.854, R.999 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.701, C:F.736, C:V.743, C:V.744, C:I.747, C:I.847 Hydrogen bonds: C:S.680, C:S.680, C:N.693, C:S.851, C:R.852, C:N.853, C:N.853, B:K.606 Salt bridges: C:R.689, C:R.852, C:R.999, B:K.606, B:K.606 PIO.10: 23 residues within 4Å: Chain C: K.606, F.873 Chain D: S.680, Y.684, R.689, N.693, I.697, L.700, F.701, F.736, F.739, S.740, V.743, V.744, I.747, I.847, F.848, V.850, S.851, R.852, N.853, L.854, R.999 19 PLIP interactions: 16 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.701, D:F.736, D:V.743, D:V.744, D:I.747, D:I.847 Hydrogen bonds: D:S.680, D:S.680, D:N.693, D:S.851, D:R.852, D:N.853, D:N.853, C:K.606 Salt bridges: D:R.689, D:R.852, D:R.999, C:K.606, C:K.606

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

ULO.2: 20 residues within 4Å: Chain A: F.739, N.742, V.743, Y.746, V.776, L.779, F.780, E.783, D.803, G.806, L.807, F.810, F.840, R.843, L.844, H.846, I.847, Y.1006, R.1009, F.1014 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:N.742, A:V.743, A:V.776, A:D.803, A:L.807, A:L.807, A:F.840, A:F.840, A:R.843, A:F.1014 Hydrogen bonds: A:R.843 ULO.5: 20 residues within 4Å: Chain B: F.739, N.742, V.743, Y.746, V.776, L.779, F.780, E.783, D.803, G.806, L.807, F.810, F.840, R.843, L.844, H.846, I.847, Y.1006, R.1009, F.1014 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.742, B:V.743, B:V.776, B:D.803, B:L.807, B:L.807, B:F.840, B:F.840, B:R.843, B:F.1014 Hydrogen bonds: B:R.843 ULO.8: 20 residues within 4Å: Chain C: F.739, N.742, V.743, Y.746, V.776, L.779, F.780, E.783, D.803, G.806, L.807, F.810, F.840, R.843, L.844, H.846, I.847, Y.1006, R.1009, F.1014 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:N.742, C:V.743, C:V.776, C:D.803, C:L.807, C:L.807, C:F.840, C:F.840, C:R.843, C:F.1014 Hydrogen bonds: C:R.843 ULO.11: 20 residues within 4Å: Chain D: F.739, N.742, V.743, Y.746, V.776, L.779, F.780, E.783, D.803, G.806, L.807, F.810, F.840, R.843, L.844, H.846, I.847, Y.1006, R.1009, F.1014 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:N.742, D:V.743, D:V.776, D:D.803, D:L.807, D:L.807, D:F.840, D:F.840, D:R.843, D:F.1014 Hydrogen bonds: D:R.843

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: Q.786, N.800, D.803 No protein-ligand interaction detected (PLIP) CA.6: 3 residues within 4Å: Chain B: Q.786, N.800, D.803 No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Chain C: Q.786, N.800, D.803 No protein-ligand interaction detected (PLIP) CA.12: 3 residues within 4Å: Chain D: Q.786, N.800, D.803 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Y. et al., Activation mechanism of the mouse cold-sensing TRPM8 channel by cooling agonist and PIP 2. Science (2022)

Release Date

2022-10-26

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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