SMTL ID : 7x6i.1

Cryo-EM structure of the human TRPC5 ion channel in complex with G alpha i3 subunits, class1

Coordinates

PDB Format Compare

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, M.438, I.484, L.491, Q.507, L.510, G.511 Chain E: T.603, T.607 Ligands: YZY.5 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:T.603, E:T.607, A:I.484, A:I.484, A:L.510 Salt bridges: A:K.645 PTY.8: 12 residues within 4Å: Chain A: T.603, T.607 Chain C: D.433, W.434, W.435, M.438, I.484, L.491, Q.507, L.510, G.511 Ligands: YZY.6 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.484, C:I.484, C:L.510, A:T.603, A:T.607 Salt bridges: C:K.645 PTY.13: 12 residues within 4Å: Chain C: T.603, T.607 Chain D: D.433, W.434, W.435, M.438, I.484, L.491, Q.507, L.510, G.511 Ligands: YZY.12 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:T.603, C:T.607, D:I.484, D:I.484, D:L.510 Salt bridges: D:K.645 PTY.18: 12 residues within 4Å: Chain D: T.603, T.607 Chain E: D.433, W.434, W.435, M.438, I.484, L.491, Q.507, L.510, G.511 Ligands: YZY.17 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:I.484, E:I.484, E:L.510, D:T.603, D:T.607 Salt bridges: E: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 E: F.522 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:T.371, A:L.375, A:F.497, A:A.499, E:F.522 Hydrogen bonds: A:Y.316 Y01.9: 11 residues within 4Å: Chain A: F.522 Chain C: 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 C, 1 interactions with chain A Hydrophobic interactions: C:T.371, C:L.375, C:F.497, C:A.499, A:F.522 Hydrogen bonds: C:Y.316 Y01.14: 11 residues within 4Å: Chain C: F.522 Chain D: 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 D, 1 interactions with chain C Hydrophobic interactions: D:T.371, D:L.375, D:F.497, D:A.499, C:F.522 Hydrogen bonds: D:Y.316 Y01.19: 11 residues within 4Å: Chain D: F.522 Chain E: 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 E, 1 interactions with chain D Hydrophobic interactions: E:T.371, E:L.375, E:F.497, E:A.499, D:F.522 Hydrogen bonds: E: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.10: 4 residues within 4Å: Chain C: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.172, C:C.176, C:C.178, C:C.181 ZN.15: 4 residues within 4Å: Chain D: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.172, D:C.176, D:C.178, D:C.181 ZN.20: 4 residues within 4Å: Chain E: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.172, E:C.176, E:C.178, E:C.181

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.418, E.421, N.436, D.439 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.418, A:D.439 CA.11: 4 residues within 4Å: Chain C: E.418, E.421, N.436, D.439 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.418, C:D.439 CA.16: 4 residues within 4Å: Chain D: E.418, E.421, N.436, D.439 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.418, D:D.439 CA.21: 4 residues within 4Å: Chain E: E.418, E.421, N.436, D.439 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.418, E:D.439

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

YZY.5: 14 residues within 4Å: Chain A: L.514, L.521, Y.524, C.525, L.528, Q.573, F.576, W.577 Chain E: F.599, T.603, T.607, V.610, I.611 Ligands: PTY.1 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:T.607, E:V.610, E:V.610, E:I.611, E:I.611, A:L.514, A:L.528, A:F.576 Hydrogen bonds: A:Q.573 YZY.6: 14 residues within 4Å: Chain A: F.599, T.603, T.607, V.610, I.611 Chain C: L.514, L.521, Y.524, C.525, L.528, Q.573, F.576, W.577 Ligands: PTY.8 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:L.514, C:L.528, C:F.576, A:T.607, A:V.610, A:V.610, A:I.611, A:I.611 Hydrogen bonds: C:Q.573 YZY.12: 14 residues within 4Å: Chain C: F.599, T.603, T.607, V.610, I.611 Chain D: L.514, L.521, Y.524, C.525, L.528, Q.573, F.576, W.577 Ligands: PTY.13 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:T.607, C:V.610, C:V.610, C:I.611, C:I.611, D:L.514, D:L.528, D:F.576 Hydrogen bonds: D:Q.573 YZY.17: 14 residues within 4Å: Chain D: F.599, T.603, T.607, V.610, I.611 Chain E: L.514, L.521, Y.524, C.525, L.528, Q.573, F.576, W.577 Ligands: PTY.18 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:L.514, E:L.528, E:F.576, D:T.607, D:V.610, D:V.610, D:I.611, D:I.611 Hydrogen bonds: E:Q.573

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

GTP.7: 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.22: 25 residues within 4Å: Chain F: 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 F Hydrogen bonds: F:A.41, F:E.43, F:S.44, F:G.45, F:K.46, F:S.47, F:T.48, F:T.48, F:S.157, F:S.157, F:R.182, F:T.187, F:T.187, F:G.209, F:N.275, F:K.276, F:K.276, F:A.332, F:T.333 Salt bridges: F:K.46, F:K.46, F:R.184, F:R.184, F:R.184, F:D.278 GTP.23: 25 residues within 4Å: Chain G: 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 G Hydrogen bonds: G:A.41, G:E.43, G:S.44, G:G.45, G:K.46, G:S.47, G:T.48, G:T.48, G:S.157, G:S.157, G:R.182, G:T.187, G:T.187, G:G.209, G:N.275, G:K.276, G:K.276, G:A.332, G:T.333 Salt bridges: G:K.46, G:K.46, G:R.184, G:R.184, G:R.184, G:D.278 GTP.24: 25 residues within 4Å: Chain H: 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 H Hydrogen bonds: H:A.41, H:E.43, H:S.44, H:G.45, H:K.46, H:S.47, H:T.48, H:T.48, H:S.157, H:S.157, H:R.182, H:T.187, H:T.187, H:G.209, H:N.275, H:K.276, H:K.276, H:A.332, H:T.333 Salt bridges: H:K.46, H:K.46, H:R.184, H:R.184, H:R.184, H: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

2023-04-26

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

D
C

E
D

B
E

F
F

G
G

H
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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