SMTL ID : 8ed8.1

cryo-EM structure of TRPM3 ion channel in the presence of PIP2 and PregS, state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.1: 12 residues within 4Å: Chain A: Y.942, W.943, L.953, V.977, I.980, Y.981, I.984, V.1000, M.1007, Q.1132 Chain G: F.1024, I.1094 11 PLIP interactions: 2 interactions with chain G, 9 interactions with chain A Hydrophobic interactions: G:F.1024, G:I.1094, A:L.953, A:V.977, A:I.980, A:Y.981, A:I.984, A:I.984, A:V.1000 Hydrogen bonds: A:Y.942, A:Q.1132 3PH.5: 15 residues within 4Å: Chain A: F.1024, I.1094, Y.1098, V.1101 Chain C: E.941, Y.942, W.943, L.953, V.977, N.978, I.980, Y.981, V.1000, M.1007, Q.1132 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:F.1024, A:I.1094, A:Y.1098, A:V.1101, C:W.943, C:L.953, C:V.977, C:I.980, C:Y.981, C:Y.981, C:V.1000 Hydrogen bonds: C:Y.942, C:Q.1132 3PH.8: 15 residues within 4Å: Chain C: S.1023, F.1024, I.1094, Y.1098, V.1101 Chain E: E.941, Y.942, W.943, V.977, I.980, Y.981, I.984, V.1000, M.1007, Q.1132 11 PLIP interactions: 7 interactions with chain E, 4 interactions with chain C Hydrophobic interactions: E:W.943, E:I.980, E:Y.981, E:I.984, E:V.1000, C:F.1024, C:I.1094, C:Y.1098, C:V.1101 Hydrogen bonds: E:Y.942, E:Q.1132 3PH.11: 15 residues within 4Å: Chain E: S.1023, F.1024, I.1094, Y.1098, V.1101 Chain G: E.941, Y.942, W.943, L.953, V.977, I.980, Y.981, V.1000, M.1007, Q.1132 13 PLIP interactions: 9 interactions with chain G, 4 interactions with chain E Hydrophobic interactions: G:W.943, G:L.953, G:V.977, G:I.980, G:Y.981, G:Y.981, G:V.1000, E:F.1024, E:I.1094, E:Y.1098, E:V.1101 Hydrogen bonds: G:Y.942, G:Q.1132

4 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.2: 7 residues within 4Å: Chain A: P.1038, S.1039, W.1040 Chain C: M.887, N.890, Y.891, Y.983 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.1040, A:W.1040, C:M.887, C:Y.891, C:Y.891 9Z9.6: 8 residues within 4Å: Chain C: P.1038, S.1039, W.1040, A.1043 Chain E: M.887, N.890, Y.891, Y.983 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:M.887, E:Y.891, C:W.1040, C:A.1043 Hydrogen bonds: E:N.890 9Z9.9: 8 residues within 4Å: Chain E: P.1038, S.1039, W.1040, A.1043 Chain G: M.887, N.890, Y.891, Y.983 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain G Hydrophobic interactions: E:W.1040, E:A.1043, G:M.887, G:Y.891 Hydrogen bonds: G:N.890 9Z9.12: 8 residues within 4Å: Chain A: M.887, N.890, Y.891, Y.983 Chain G: P.1038, S.1039, W.1040, A.1043 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: G:W.1040, G:A.1043, A:M.887, A:Y.891 Hydrogen bonds: A:N.890

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.3: 10 residues within 4Å: Chain A: S.773, G.774, L.775, F.875, W.876, I.989, F.990, N.993, K.994, Y.995 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.875, A:I.989, A:F.990, A:F.990 Hydrogen bonds: A:L.775, A:Y.995 Salt bridges: A:K.994, A:K.994 PIO.7: 10 residues within 4Å: Chain C: S.773, G.774, L.775, I.778, W.876, I.989, F.990, N.993, K.994, Y.995 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.775, C:I.778, C:I.989, C:F.990, C:N.993 Hydrogen bonds: C:S.773, C:N.993, C:Y.995 Salt bridges: C:K.994, C:K.994 PIO.10: 11 residues within 4Å: Chain E: S.773, I.778, F.875, W.876, T.879, I.989, F.990, V.992, N.993, K.994, Y.995 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:I.778, E:F.875, E:W.876, E:T.879, E:F.990 Hydrogen bonds: E:S.773, E:Y.995 Salt bridges: E:K.994, E:K.994 PIO.13: 9 residues within 4Å: Chain G: S.773, L.775, I.778, W.876, I.989, F.990, N.993, K.994, Y.995 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:L.775, G:I.778, G:W.876, G:I.989, G:F.990, G:F.990 Hydrogen bonds: G:K.771, G:S.773, G:Y.995 Salt bridges: G:K.994, G:K.994

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, C. et al., Structural and functional analyses of a GPCR-inhibited ion channel TRPM3. Neuron (2023)

Release Date

2022-11-02

Peptides

Transient receptor potential cation channel, subfamily M, member 3: ACEG
Unidentified segment at the N-terminus of TRPM3: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
D

B
E

D
F

F
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel, subfamily M, member 3

Unidentified segment at the N-terminus of TRPM3

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