SMTL ID : 9b2a.1

Cryo-EM structure of the mouse TRPM3 alpha 2 channel in complex with the neurosteroid pregnenolone sulfate and the synthetic agonist CIM 0216

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 01: (2S)-2-(3,4-dihydroquinolin-1(2H)-yl)-N-(5-methyl-1,2-oxazol-3-yl)-2-phenylacetamide

01.1: 16 residues within 4Å: Chain A: Y.878, T.879, Y.882, Y.911, L.915, E.918, K.919, E.922, W.982, R.985, L.986, I.989, T.1139, F.1140, R.1143, P.1148 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.882, A:Y.882, A:L.915, A:E.918, A:K.919, A:I.989, A:P.1148 Hydrogen bonds: A:T.879 pi-Cation interactions: A:K.919 01.4: 16 residues within 4Å: Chain B: Y.878, T.879, Y.882, Y.911, L.915, E.918, K.919, E.922, W.982, R.985, L.986, I.989, T.1139, F.1140, R.1143, P.1148 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.882, B:Y.882, B:L.915, B:E.918, B:K.919, B:I.989, B:P.1148 Hydrogen bonds: B:T.879 pi-Cation interactions: B:K.919 01.7: 16 residues within 4Å: Chain C: Y.878, T.879, Y.882, Y.911, L.915, E.918, K.919, E.922, W.982, R.985, L.986, I.989, T.1139, F.1140, R.1143, P.1148 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.882, C:Y.882, C:L.915, C:E.918, C:K.919, C:I.989, C:P.1148 Hydrogen bonds: C:T.879 pi-Cation interactions: C:K.919 01.10: 16 residues within 4Å: Chain D: Y.878, T.879, Y.882, Y.911, L.915, E.918, K.919, E.922, W.982, R.985, L.986, I.989, T.1139, F.1140, R.1143, P.1148 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.882, D:Y.882, D:L.915, D:E.918, D:K.919, D:I.989, D:P.1148 Hydrogen bonds: D:T.879 pi-Cation interactions: D:K.919

4 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.2: 16 residues within 4Å: Chain A: Y.942, W.943, I.984, L.987, V.1000, M.1001, I.1003, G.1004, M.1007, M.1010 Chain B: V.1020, F.1024, Y.1098, V.1101, A.1102, L.1105 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.1098 6OU.5: 16 residues within 4Å: Chain B: Y.942, W.943, I.984, L.987, V.1000, M.1001, I.1003, G.1004, M.1007, M.1010 Chain C: V.1020, F.1024, Y.1098, V.1101, A.1102, L.1105 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.1098 6OU.8: 16 residues within 4Å: Chain C: Y.942, W.943, I.984, L.987, V.1000, M.1001, I.1003, G.1004, M.1007, M.1010 Chain D: V.1020, F.1024, Y.1098, V.1101, A.1102, L.1105 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.1098 6OU.11: 16 residues within 4Å: Chain A: V.1020, F.1024, Y.1098, V.1101, A.1102, L.1105 Chain D: Y.942, W.943, I.984, L.987, V.1000, M.1001, I.1003, G.1004, M.1007, M.1010 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.1098, A:V.1101

4 x A8W: Pregnenolone sulfate(Non-covalent)

A8W.3: 12 residues within 4Å: Chain A: M.1022, V.1026, P.1038, S.1039, W.1040, L.1042, I.1046 Chain D: M.887, N.890, Y.891, L.894, Y.983 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:P.1038, D:Y.891 Hydrogen bonds: A:W.1040 A8W.6: 12 residues within 4Å: Chain A: M.887, N.890, Y.891, L.894, Y.983 Chain B: M.1022, V.1026, P.1038, S.1039, W.1040, L.1042, I.1046 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.1038, A:Y.891 Hydrogen bonds: B:W.1040 A8W.9: 12 residues within 4Å: Chain B: M.887, N.890, Y.891, L.894, Y.983 Chain C: M.1022, V.1026, P.1038, S.1039, W.1040, L.1042, I.1046 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.891, C:P.1038 Hydrogen bonds: C:W.1040 A8W.12: 12 residues within 4Å: Chain C: M.887, N.890, Y.891, L.894, Y.983 Chain D: M.1022, V.1026, P.1038, S.1039, W.1040, L.1042, I.1046 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.1038, C:Y.891 Hydrogen bonds: D:W.1040

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Y. et al., Molecular basis of neurosteroid and anticonvulsant regulation of TRPM3. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-01-22

Peptides

Transient receptor potential cation channel, subfamily M, member 3: 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 3

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