SMTL ID : 9b29.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

6OU.1: 26 residues within 4Å: Chain A: Y.942, W.943, T.946, I.949, A.950, L.953, V.977, I.980, Y.981, I.984, L.987, V.1000, M.1001, I.1003, G.1004, M.1007 Chain B: V.1020, F.1024, W.1089, I.1090, A.1093, I.1094, C.1097, Y.1098, V.1101 Ligands: LBN.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.949, A:I.980, A:I.984, B:I.1094 Hydrogen bonds: A:W.943 6OU.6: 26 residues within 4Å: Chain B: Y.942, W.943, T.946, I.949, A.950, L.953, V.977, I.980, Y.981, I.984, L.987, V.1000, M.1001, I.1003, G.1004, M.1007 Chain C: V.1020, F.1024, W.1089, I.1090, A.1093, I.1094, C.1097, Y.1098, V.1101 Ligands: LBN.7 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.1094, B:I.949, B:I.980, B:I.984 Hydrogen bonds: B:W.943 6OU.11: 26 residues within 4Å: Chain C: Y.942, W.943, T.946, I.949, A.950, L.953, V.977, I.980, Y.981, I.984, L.987, V.1000, M.1001, I.1003, G.1004, M.1007 Chain D: V.1020, F.1024, W.1089, I.1090, A.1093, I.1094, C.1097, Y.1098, V.1101 Ligands: LBN.12 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.949, C:I.980, C:I.984, D:I.1094 Hydrogen bonds: C:W.943 6OU.16: 26 residues within 4Å: Chain A: V.1020, F.1024, W.1089, I.1090, A.1093, I.1094, C.1097, Y.1098, V.1101 Chain D: Y.942, W.943, T.946, I.949, A.950, L.953, V.977, I.980, Y.981, I.984, L.987, V.1000, M.1001, I.1003, G.1004, M.1007 Ligands: LBN.17 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.949, D:I.980, D:I.984, A:I.1094 Hydrogen bonds: D:W.943

4 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.2: 12 residues within 4Å: Chain A: L.953, D.970, V.973, I.974, V.977 Chain B: C.1084, K.1085, T.1086, G.1087, W.1089, I.1090 Ligands: 6OU.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.953, B:W.1089 Hydrogen bonds: B:W.1089 LBN.7: 12 residues within 4Å: Chain B: L.953, D.970, V.973, I.974, V.977 Chain C: C.1084, K.1085, T.1086, G.1087, W.1089, I.1090 Ligands: 6OU.6 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.1089, B:L.953 Hydrogen bonds: C:W.1089 LBN.12: 12 residues within 4Å: Chain C: L.953, D.970, V.973, I.974, V.977 Chain D: C.1084, K.1085, T.1086, G.1087, W.1089, I.1090 Ligands: 6OU.11 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.953, D:W.1089 Hydrogen bonds: D:W.1089 LBN.17: 12 residues within 4Å: Chain A: C.1084, K.1085, T.1086, G.1087, W.1089, I.1090 Chain D: L.953, D.970, V.973, I.974, V.977 Ligands: 6OU.16 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.1089, D:L.953 Hydrogen bonds: A:W.1089

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 16 residues within 4Å: Chain A: V.1014, M.1017, L.1018, L.1021, K.1044, F.1047, Y.1048, Y.1051, W.1052 Chain B: D.1064, W.1089, P.1092, A.1093, A.1096, L.1100 Ligands: PX2.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.1014, A:L.1018, A:F.1047, A:Y.1051 Salt bridges: A:K.1044, A:K.1044 Y01.4: 14 residues within 4Å: Chain A: M.1022, 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 Y01.8: 16 residues within 4Å: Chain B: V.1014, M.1017, 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 Ligands: PX2.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.1014, B:L.1018, B:F.1047, B:Y.1051 Salt bridges: B:K.1044, B:K.1044 Y01.9: 14 residues within 4Å: Chain A: I.883, L.886, M.887, N.890, Y.891, L.894, Y.983 Chain B: M.1022, P.1038, S.1039, W.1040, L.1042, A.1043, I.1046 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.1040, A:Y.891 Y01.13: 16 residues within 4Å: Chain C: V.1014, M.1017, 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 Ligands: PX2.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.1014, C:L.1018, C:F.1047, C:Y.1051 Salt bridges: C:K.1044, C:K.1044 Y01.14: 14 residues within 4Å: Chain B: I.883, L.886, M.887, N.890, Y.891, L.894, Y.983 Chain C: M.1022, P.1038, S.1039, W.1040, L.1042, A.1043, I.1046 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.1040, B:Y.891 Y01.18: 16 residues within 4Å: Chain A: D.1064, W.1089, P.1092, A.1093, A.1096, L.1100 Chain D: V.1014, M.1017, L.1018, L.1021, K.1044, F.1047, Y.1048, Y.1051, W.1052 Ligands: PX2.20 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.1014, D:L.1018, D:F.1047, D:Y.1051 Salt bridges: D:K.1044, D:K.1044 Y01.19: 14 residues within 4Å: Chain C: I.883, L.886, M.887, N.890, Y.891, L.894, Y.983 Chain D: M.1022, P.1038, S.1039, W.1040, L.1042, A.1043, I.1046 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.1040, C:Y.891

4 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX2.5: 7 residues within 4Å: Chain A: L.1018, W.1040, K.1041, A.1043, K.1044, F.1047 Ligands: Y01.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.1044 PX2.10: 7 residues within 4Å: Chain B: L.1018, W.1040, K.1041, A.1043, K.1044, F.1047 Ligands: Y01.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.1044 PX2.15: 7 residues within 4Å: Chain C: L.1018, W.1040, K.1041, A.1043, K.1044, F.1047 Ligands: Y01.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.1044 PX2.20: 7 residues within 4Å: Chain D: L.1018, W.1040, K.1041, A.1043, K.1044, F.1047 Ligands: Y01.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.1044

Links

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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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