SMTL ID : 9b28.1

Cryo-EM structure of the mouse TRPM3 alpha 2 channel in complex with primidone

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 14 residues within 4Å: Chain A: V.1014, L.1018, L.1021, K.1044, F.1047, Y.1048, Y.1051, W.1052 Chain C: D.1064, W.1089, P.1092, A.1093, A.1096, L.1100 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:K.1044, A:F.1047, A:Y.1048, A:Y.1051, C:W.1089, C:P.1092, C:A.1093, C:L.1100 Y01.4: 13 residues within 4Å: Chain A: P.1038, S.1039, W.1040, L.1042, A.1043, I.1046 Chain D: I.883, L.886, M.887, N.890, Y.891, L.894, Y.983 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:Y.891, A:W.1040 Y01.5: 14 residues within 4Å: Chain B: V.1014, L.1018, L.1021, K.1044, F.1047, Y.1048, Y.1051, W.1052 Chain D: D.1064, W.1089, P.1092, A.1093, A.1096, L.1100 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:W.1089, D:P.1092, D:A.1093, D:L.1100, B:K.1044, B:F.1047, B:Y.1048, B:Y.1051 Y01.8: 13 residues within 4Å: Chain B: P.1038, S.1039, W.1040, L.1042, A.1043, I.1046 Chain C: I.883, L.886, M.887, N.890, Y.891, L.894, Y.983 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.1040, C:Y.891 Y01.9: 14 residues within 4Å: Chain B: D.1064, W.1089, P.1092, A.1093, A.1096, L.1100 Chain C: V.1014, L.1018, L.1021, K.1044, F.1047, Y.1048, Y.1051, W.1052 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:K.1044, C:F.1047, C:Y.1048, C:Y.1051, B:W.1089, B:P.1092, B:A.1093, B:L.1100 Y01.12: 13 residues within 4Å: Chain A: I.883, L.886, M.887, N.890, Y.891, L.894, Y.983 Chain C: P.1038, S.1039, W.1040, L.1042, A.1043, I.1046 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.1040, A:Y.891 Y01.13: 14 residues within 4Å: Chain A: D.1064, W.1089, P.1092, A.1093, A.1096, L.1100 Chain D: V.1014, L.1018, L.1021, K.1044, F.1047, Y.1048, Y.1051, W.1052 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:K.1044, D:F.1047, D:Y.1048, D:Y.1051, A:W.1089, A:P.1092, A:A.1093, A:L.1100 Y01.16: 13 residues within 4Å: Chain B: I.883, L.886, M.887, N.890, Y.891, L.894, Y.983 Chain D: P.1038, S.1039, W.1040, L.1042, A.1043, I.1046 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.891, D:W.1040

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

6OU.2: 19 residues within 4Å: Chain A: Q.940, E.941, Y.942, W.943, T.946, I.980, Y.981, I.984, L.987, V.1000, M.1001, I.1003, G.1004, K.1005, M.1007, V.1128, Q.1132 Chain C: C.1097, V.1101 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.943, A:I.984 Hydrogen bonds: A:Y.942 6OU.6: 19 residues within 4Å: Chain B: Q.940, E.941, Y.942, W.943, T.946, I.980, Y.981, I.984, L.987, V.1000, M.1001, I.1003, G.1004, K.1005, M.1007, V.1128, Q.1132 Chain D: C.1097, V.1101 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.943, B:I.984 Hydrogen bonds: B:Y.942 6OU.10: 19 residues within 4Å: Chain B: C.1097, V.1101 Chain C: Q.940, E.941, Y.942, W.943, T.946, I.980, Y.981, I.984, L.987, V.1000, M.1001, I.1003, G.1004, K.1005, M.1007, V.1128, Q.1132 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.943, C:I.984 Hydrogen bonds: C:Y.942 6OU.14: 19 residues within 4Å: Chain A: C.1097, V.1101 Chain D: Q.940, E.941, Y.942, W.943, T.946, I.980, Y.981, I.984, L.987, V.1000, M.1001, I.1003, G.1004, K.1005, M.1007, V.1128, Q.1132 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.943, D:I.984 Hydrogen bonds: D:Y.942

4 x 01: primidone

01.3: 14 residues within 4Å: Chain A: F.875, Y.878, T.879, Y.882, Y.911, L.915, K.919, D.947, R.985, D.988, I.989, F.1140, R.1143, P.1148 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.875, A:Y.878, A:I.989, A:I.989 Hydrogen bonds: A:Y.911 pi-Stacking: A:F.1140 01.7: 14 residues within 4Å: Chain B: F.875, Y.878, T.879, Y.882, Y.911, L.915, K.919, D.947, R.985, D.988, I.989, F.1140, R.1143, P.1148 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.875, B:Y.878, B:I.989, B:I.989 Hydrogen bonds: B:Y.911 pi-Stacking: B:F.1140 01.11: 14 residues within 4Å: Chain C: F.875, Y.878, T.879, Y.882, Y.911, L.915, K.919, D.947, R.985, D.988, I.989, F.1140, R.1143, P.1148 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.875, C:Y.878, C:I.989, C:I.989 Hydrogen bonds: C:Y.911 pi-Stacking: C:F.1140 01.15: 14 residues within 4Å: Chain D: F.875, Y.878, T.879, Y.882, Y.911, L.915, K.919, D.947, R.985, D.988, I.989, F.1140, R.1143, P.1148 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.875, D:Y.878, D:I.989, D:I.989 Hydrogen bonds: D:Y.911 pi-Stacking: D:F.1140

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
C

C
B

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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