SMTL ID : 8gvx.1

Cryo-EM structure of the human TRPC5 ion channel in complex with G alpha i3 subunits, class2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 12 residues within 4Å: Chain A: D.433, W.434, W.435, I.484, L.491, Q.507, L.510, G.511, L.514 Chain F: T.603, T.607 Ligands: YZY.5 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:I.484, A:I.484, A:L.510, A:L.514, F:T.603, F:T.607 Salt bridges: A:K.645 PTY.10: 12 residues within 4Å: Chain F: D.433, W.434, W.435, I.484, L.491, Q.507, L.510, G.511, L.514 Chain H: T.603, T.607 Ligands: YZY.14 7 PLIP interactions: 2 interactions with chain H, 5 interactions with chain F Hydrophobic interactions: H:T.603, H:T.607, F:I.484, F:I.484, F:L.510, F:L.514 Salt bridges: F:K.645 PTY.15: 12 residues within 4Å: Chain A: T.603, T.607 Chain G: D.433, W.434, W.435, I.484, L.491, Q.507, L.510, G.511, L.514 Ligands: YZY.19 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: A:T.603, A:T.607, G:I.484, G:I.484, G:L.510, G:L.514 Salt bridges: G:K.645 PTY.20: 12 residues within 4Å: Chain G: T.603, T.607 Chain H: D.433, W.434, W.435, I.484, L.491, Q.507, L.510, G.511, L.514 Ligands: YZY.24 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:I.484, H:I.484, H:L.510, H:L.514, G:T.603, G:T.607 Salt bridges: H:K.645

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 11 residues within 4Å: Chain A: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 Chain F: F.522 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:T.371, A:L.375, A:F.497, A:A.499, F:F.522 Hydrogen bonds: A:Y.316 Y01.11: 11 residues within 4Å: Chain F: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 Chain H: F.522 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: F:T.371, F:L.375, F:F.497, F:A.499, H:F.522 Hydrogen bonds: F:Y.316 Y01.16: 11 residues within 4Å: Chain A: F.522 Chain G: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: A:F.522, G:T.371, G:L.375, G:F.497, G:A.499 Hydrogen bonds: G:Y.316 Y01.21: 11 residues within 4Å: Chain G: F.522 Chain H: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 6 PLIP interactions: 5 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:T.371, H:L.375, H:F.497, H:A.499, G:F.522 Hydrogen bonds: H:Y.316

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.172, A:C.176, A:C.178, A:C.181 ZN.12: 4 residues within 4Å: Chain F: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.172, F:C.176, F:C.178, F:C.181 ZN.17: 4 residues within 4Å: Chain G: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.172, G:C.176, G:C.178, G:C.181 ZN.22: 4 residues within 4Å: Chain H: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.172, H:C.176, H:C.178, H:C.181

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.418, A:D.439 CA.13: 5 residues within 4Å: Chain F: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.418, F:D.439 CA.18: 5 residues within 4Å: Chain G: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:E.418, G:D.439 CA.23: 5 residues within 4Å: Chain H: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.418, H:D.439

4 x YZY: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

YZY.5: 16 residues within 4Å: Chain A: L.514, L.521, Y.524, C.525, L.528, F.569, Q.573, F.576, F.580 Chain F: F.599, A.602, T.603, T.607, V.610, I.611 Ligands: PTY.1 9 PLIP interactions: 4 interactions with chain F, 5 interactions with chain A Hydrophobic interactions: F:T.607, F:V.610, F:I.611, F:I.611, A:L.514, A:L.528, A:F.576, A:F.580 Hydrogen bonds: A:Q.573 YZY.14: 16 residues within 4Å: Chain F: L.514, L.521, Y.524, C.525, L.528, F.569, Q.573, F.576, F.580 Chain H: F.599, A.602, T.603, T.607, V.610, I.611 Ligands: PTY.10 10 PLIP interactions: 5 interactions with chain H, 5 interactions with chain F Hydrophobic interactions: H:T.607, H:V.610, H:V.610, H:I.611, H:I.611, F:L.514, F:L.528, F:F.576, F:F.580 Hydrogen bonds: F:Q.573 YZY.19: 16 residues within 4Å: Chain A: F.599, A.602, T.603, T.607, V.610, I.611 Chain G: L.514, L.521, Y.524, C.525, L.528, F.569, Q.573, F.576, F.580 Ligands: PTY.15 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain A Hydrophobic interactions: G:L.514, G:L.528, G:F.576, G:F.580, A:T.607, A:V.610, A:V.610, A:I.611, A:I.611 Hydrogen bonds: G:Q.573 YZY.24: 16 residues within 4Å: Chain G: F.599, A.602, T.603, T.607, V.610, I.611 Chain H: L.514, L.521, Y.524, C.525, L.528, F.569, Q.573, F.576, F.580 Ligands: PTY.20 10 PLIP interactions: 5 interactions with chain G, 5 interactions with chain H Hydrophobic interactions: G:T.607, G:V.610, G:V.610, G:I.611, G:I.611, H:L.514, H:L.528, H:F.576, H:F.580 Hydrogen bonds: H:Q.573

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.6: 25 residues within 4Å: Chain B: G.42, E.43, S.44, G.45, K.46, S.47, T.48, D.156, S.157, L.181, R.182, T.183, R.184, V.185, K.186, T.187, V.207, G.209, N.275, K.276, D.278, L.279, C.331, A.332, T.333 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:A.41, B:E.43, B:S.44, B:G.45, B:K.46, B:S.47, B:T.48, B:T.48, B:S.157, B:S.157, B:R.182, B:T.187, B:T.187, B:G.209, B:N.275, B:K.276, B:K.276, B:A.332, B:T.333 Salt bridges: B:K.46, B:K.46, B:R.184, B:R.184, B:R.184, B:D.278 GTP.7: 25 residues within 4Å: Chain C: G.42, E.43, S.44, G.45, K.46, S.47, T.48, D.156, S.157, L.181, R.182, T.183, R.184, V.185, K.186, T.187, V.207, G.209, N.275, K.276, D.278, L.279, C.331, A.332, T.333 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:A.41, C:E.43, C:S.44, C:G.45, C:K.46, C:S.47, C:T.48, C:T.48, C:S.157, C:S.157, C:R.182, C:T.187, C:T.187, C:G.209, C:N.275, C:K.276, C:K.276, C:A.332, C:T.333 Salt bridges: C:K.46, C:K.46, C:R.184, C:R.184, C:R.184, C:D.278 GTP.8: 25 residues within 4Å: Chain D: G.42, E.43, S.44, G.45, K.46, S.47, T.48, D.156, S.157, L.181, R.182, T.183, R.184, V.185, K.186, T.187, V.207, G.209, N.275, K.276, D.278, L.279, C.331, A.332, T.333 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:A.41, D:E.43, D:S.44, D:G.45, D:K.46, D:S.47, D:T.48, D:T.48, D:S.157, D:S.157, D:R.182, D:T.187, D:T.187, D:G.209, D:N.275, D:K.276, D:K.276, D:A.332, D:T.333 Salt bridges: D:K.46, D:K.46, D:R.184, D:R.184, D:R.184, D:D.278 GTP.9: 25 residues within 4Å: Chain E: G.42, E.43, S.44, G.45, K.46, S.47, T.48, D.156, S.157, L.181, R.182, T.183, R.184, V.185, K.186, T.187, V.207, G.209, N.275, K.276, D.278, L.279, C.331, A.332, T.333 25 PLIP interactions: 25 interactions with chain E Hydrogen bonds: E:A.41, E:E.43, E:S.44, E:G.45, E:K.46, E:S.47, E:T.48, E:T.48, E:S.157, E:S.157, E:R.182, E:T.187, E:T.187, E:G.209, E:N.275, E:K.276, E:K.276, E:A.332, E:T.333 Salt bridges: E:K.46, E:K.46, E:R.184, E:R.184, E:R.184, E:D.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Won, J. et al., Molecular architecture of the G alpha i -bound TRPC5 ion channel. Nat Commun (2023)

Release Date

2023-05-24

Peptides

Short transient receptor potential channel 5: AFGH
Guanine nucleotide-binding protein G(i) subunit alpha-3: BCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

F
A

G
C

H
D

B
F

C
E

D
G

E
H

Membrane

We predict this structure to be a membrane protein.
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Short transient receptor potential channel 5

Guanine nucleotide-binding protein G(i) subunit alpha-3

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