SMTL ID : 8ddx.1

cryo-EM structure of TRPM3 ion channel in complex with Gbg in the presence of PIP2, tethered by ALFA-nanobody

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-1-1-mer

Ligands

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

3PH.1: 13 residues within 4Å: Chain A: Y.941, W.942, I.948, V.976, I.979, Y.980, I.983, L.986, V.999, I.1002 Chain G: F.1023, I.1093, Y.1097 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain G Hydrophobic interactions: A:I.948, A:V.976, A:I.979, A:I.983, A:I.983, A:L.986, A:V.999, A:I.1002, G:F.1023, G:I.1093, G:Y.1097 Hydrogen bonds: A:Y.941 3PH.5: 14 residues within 4Å: Chain A: I.1093, V.1100 Chain C: E.940, Y.941, W.942, I.948, I.979, Y.980, I.983, L.986, V.999, I.1002, G.1003, M.1006 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.948, C:I.979, C:Y.980, C:Y.980, C:I.983, C:I.983, C:L.986, C:V.999, C:I.1002, A:I.1093, A:V.1100 Hydrogen bonds: C:Q.1131 3PH.8: 14 residues within 4Å: Chain C: S.1022, Y.1097, V.1100 Chain E: E.940, Y.941, W.942, V.976, I.979, Y.980, I.983, L.986, V.999, M.1006, Q.1131 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:V.976, E:I.979, E:I.983, E:I.983, E:L.986, E:V.999, C:Y.1097, C:V.1100 Hydrogen bonds: E:Y.941, E:Q.1131 3PH.12: 13 residues within 4Å: Chain E: S.1022, F.1023 Chain G: Y.941, W.942, T.945, I.948, V.976, I.979, Y.980, I.983, V.999, M.1006, Q.1131 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:W.942, G:T.945, G:I.948, G:I.979, G:Y.980, G:Y.980, G:I.983, G:I.983, G:V.999, E:F.1023 Hydrogen bonds: G:Q.1131

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.2: 10 residues within 4Å: Chain A: K.770, S.772, G.773, W.875, I.882, I.988, F.989, N.992, K.993, Y.994 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.882, A:F.989, A:F.989 Hydrogen bonds: A:K.770, A:S.772, A:Y.994, A:Y.994 Salt bridges: A:K.993, A:K.993 PIO.6: 10 residues within 4Å: Chain C: K.770, S.772, G.773, W.875, I.988, F.989, V.991, N.992, K.993, Y.994 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.988, C:F.989, C:F.989, C:V.991 Hydrogen bonds: C:N.992, C:Y.994 Salt bridges: C:K.993, C:K.993 PIO.10: 10 residues within 4Å: Chain E: S.772, G.773, W.875, T.878, I.988, F.989, V.991, N.992, K.993, Y.994 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:W.875, E:T.878, E:I.988, E:F.989 Hydrogen bonds: E:G.773, E:Y.994, E:Y.994 Salt bridges: E:K.993, E:K.993 PIO.13: 7 residues within 4Å: Chain G: W.875, T.878, I.988, F.989, N.992, K.993, Y.994 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:W.875, G:T.878, G:I.988, G:F.989 Salt bridges: G:K.993, G:K.993

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

9Z9.3: 7 residues within 4Å: Chain A: M.886, N.889, Y.890, Y.982 Chain G: P.1037, S.1038, W.1039 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:N.889, A:Y.890, A:Y.890, G:W.1039 Hydrogen bonds: A:N.889 9Z9.4: 7 residues within 4Å: Chain A: P.1037, S.1038, W.1039 Chain C: M.886, N.889, Y.890, Y.982 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:M.886, C:Y.890, A:W.1039 9Z9.7: 8 residues within 4Å: Chain C: M.1021, P.1037, S.1038, W.1039 Chain E: M.886, N.889, Y.890, Y.982 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:M.886, E:Y.890, C:W.1039 Hydrogen bonds: E:N.889 9Z9.9: 7 residues within 4Å: Chain E: P.1037, S.1038, W.1039 Chain G: M.886, N.889, Y.890, Y.982 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:M.886, G:Y.890, G:Y.890, E:W.1039 Hydrogen bonds: G:N.889

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

NA.11: 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
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: I
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
D

B
E

D
F

F
G

H
H

I
I

J
J

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

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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