SMTL ID : 8ddt.1

cryo-EM structure of TRPM3 ion channel in the presence of PIP2, state2

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, I.949, L.953, V.977, I.980, Y.981, I.984, V.1000 Chain G: F.1024, I.1094, Y.1098 14 PLIP interactions: 3 interactions with chain G, 11 interactions with chain A Hydrophobic interactions: G:F.1024, G:I.1094, G:Y.1098, A:W.943, A:I.949, A:L.953, A:V.977, A:Y.981, A:Y.981, A:I.984, A:I.984, A:V.1000 Hydrogen bonds: A:Y.942, A:W.943 3PH.4: 16 residues within 4Å: Chain A: F.1024, I.1094, Y.1098, V.1101 Chain C: E.941, Y.942, W.943, I.949, L.953, V.977, I.980, Y.981, V.1000, I.1003, M.1007, Q.1132 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:W.943, C:I.949, C:L.953, C:Y.981, C:V.1000, C:I.1003, A:F.1024, A:I.1094, A:Y.1098, A:V.1101 Hydrogen bonds: C:E.941, C:E.941, C:Q.1132 3PH.8: 15 residues within 4Å: Chain C: F.1024, I.1094, Y.1098, V.1101 Chain E: E.941, Y.942, W.943, I.949, V.977, I.980, Y.981, V.1000, I.1003, M.1007, Q.1132 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain E Hydrophobic interactions: C:F.1024, C:I.1094, C:Y.1098, C:V.1101, E:W.943, E:I.949, E:Y.981, E:V.1000, E:I.1003 Hydrogen bonds: E:Q.1132 3PH.11: 16 residues within 4Å: Chain E: F.1024, I.1094, Y.1098, V.1101 Chain G: E.941, Y.942, W.943, I.949, L.953, V.977, I.980, Y.981, V.1000, I.1003, M.1007, Q.1132 12 PLIP interactions: 4 interactions with chain E, 8 interactions with chain G Hydrophobic interactions: E:F.1024, E:I.1094, E:Y.1098, E:V.1101, G:W.943, G:I.949, G:L.953, G:I.980, G:Y.981, G:V.1000, G:I.1003 Hydrogen bonds: 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 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:M.887, C:Y.891, A:W.1040 9Z9.5: 7 residues within 4Å: Chain C: P.1038, S.1039, W.1040, A.1043 Chain E: M.887, N.890, Y.983 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:W.1040, C:A.1043, E:M.887 Hydrogen bonds: E:N.890 9Z9.9: 7 residues within 4Å: Chain E: P.1038, S.1039, W.1040, A.1043 Chain G: M.887, N.890, Y.983 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain E Hydrophobic interactions: G:M.887, E:W.1040, E:W.1040, E:A.1043 Hydrogen bonds: G:N.890 9Z9.12: 6 residues within 4Å: Chain A: M.887, N.890, Y.983 Chain G: P.1038, S.1039, W.1040 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:M.887, G:W.1040, G:W.1040 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: 9 residues within 4Å: Chain A: S.773, G.774, L.775, W.876, I.989, F.990, N.993, K.994, Y.995 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.876, A:I.989, A:F.990, A:N.993 Hydrogen bonds: A:S.773, A:S.773 Salt bridges: A:K.994, A:K.994 PIO.6: 7 residues within 4Å: Chain C: S.773, G.774, W.876, I.989, F.990, N.993, K.994 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.989, C:F.990, C:N.993 Hydrogen bonds: C:S.773, C:S.773, C:S.773, C:N.993 Salt bridges: C:K.994, C:K.994 PIO.10: 11 residues within 4Å: Chain E: S.773, F.875, W.876, T.879, I.883, I.989, F.990, V.992, N.993, K.994, Y.995 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.875, E:T.879, E:I.883, E:F.990, E:F.990 Hydrogen bonds: E:S.773 Salt bridges: E:K.994, E:K.994 PIO.13: 9 residues within 4Å: Chain G: S.773, G.774, W.876, I.883, I.989, F.990, N.993, K.994, Y.995 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:W.876, G:W.876, G:I.883, G:I.989, G:F.990, G:F.990 Hydrogen bonds: G:S.773, G:S.773 Salt bridges: G:K.994, G:K.994

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

NA.7: 2 residues within 4Å: Chain C: G.1056 Chain E: G.1056 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.
Show / Hide

Transient receptor potential cation channel, subfamily M, member 3

Unidentified segment at the N-terminus of TRPM3

Related Entries With Identical Sequence