SMTL ID : 8gvw.1

Cryo-EM structure of the human TRPC5 ion channel in lipid nanodiscs, class2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 13 residues within 4Å: Chain A: D.433, W.434, W.435, M.438, I.484, L.491, Q.507, L.514 Chain D: T.603, M.604, T.607 Ligands: POV.2, YZY.6 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:T.603, D:T.607, A:I.484, A:I.484, A:L.491, A:L.514 Hydrogen bonds: A:D.433, A:Q.507 PTY.8: 13 residues within 4Å: Chain A: T.603, M.604, T.607 Chain B: D.433, W.434, W.435, M.438, I.484, L.491, Q.507, L.514 Ligands: YZY.7, POV.9 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.484, B:I.484, B:L.491, B:L.514, A:T.603, A:T.607 Hydrogen bonds: B:D.433, B:Q.507 PTY.14: 13 residues within 4Å: Chain B: T.603, M.604, T.607 Chain C: D.433, W.434, W.435, M.438, I.484, L.491, Q.507, L.514 Ligands: YZY.13, POV.15 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.484, C:I.484, C:L.491, C:L.514, B:T.603, B:T.607 Hydrogen bonds: C:D.433, C:Q.507 PTY.20: 13 residues within 4Å: Chain C: T.603, M.604, T.607 Chain D: D.433, W.434, W.435, M.438, I.484, L.491, Q.507, L.514 Ligands: YZY.19, POV.21 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.484, D:I.484, D:L.491, D:L.514, C:T.603, C:T.607 Hydrogen bonds: D:D.433, D:Q.507

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.2: 7 residues within 4Å: Chain A: S.444, L.445, A.448, W.472, I.477, L.481 Ligands: PTY.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.445, A:A.448, A:W.472, A:L.481, A:L.481 Hydrogen bonds: A:W.472 POV.9: 7 residues within 4Å: Chain B: S.444, L.445, A.448, W.472, I.477, L.481 Ligands: PTY.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.445, B:A.448, B:W.472, B:L.481, B:L.481 Hydrogen bonds: B:W.472 POV.15: 7 residues within 4Å: Chain C: S.444, L.445, A.448, W.472, I.477, L.481 Ligands: PTY.14 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.445, C:A.448, C:W.472, C:L.481, C:L.481 Hydrogen bonds: C:W.472 POV.21: 7 residues within 4Å: Chain D: S.444, L.445, A.448, W.472, I.477, L.481 Ligands: PTY.20 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.445, D:A.448, D:W.472, D:L.481, D:L.481 Hydrogen bonds: D:W.472

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 13 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 D: F.522, C.525, L.526 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.371, A:L.375, A:L.493, A:L.496, D:L.526 Hydrogen bonds: A:Y.316, A:Y.316, A:N.500 Y01.10: 13 residues within 4Å: Chain A: F.522, C.525, L.526 Chain B: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.526, B:T.371, B:L.375, B:L.493, B:L.496 Hydrogen bonds: B:Y.316, B:Y.316, B:N.500 Y01.16: 13 residues within 4Å: Chain B: F.522, C.525, L.526 Chain C: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.371, C:L.375, C:L.493, C:L.496, B:L.526 Hydrogen bonds: C:Y.316, C:Y.316, C:N.500 Y01.22: 13 residues within 4Å: Chain C: F.522, C.525, L.526 Chain D: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499, N.500 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:T.371, D:L.375, D:L.493, D:L.496, C:L.526 Hydrogen bonds: D:Y.316, D:Y.316, D:N.500

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.11: 4 residues within 4Å: Chain B: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.172, B:C.176, B:C.178, B:C.181 ZN.17: 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.23: 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

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: E.418, E.421, N.436, D.439, R.492 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.418, A:E.421, A:D.439 CA.12: 5 residues within 4Å: Chain B: E.418, E.421, N.436, D.439, R.492 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.418, B:E.421, B:D.439 CA.18: 5 residues within 4Å: Chain C: E.418, E.421, N.436, D.439, R.492 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.418, C:E.421, C:D.439 CA.24: 5 residues within 4Å: Chain D: E.418, E.421, N.436, D.439, R.492 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.418, D:E.421, D:D.439

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

YZY.6: 12 residues within 4Å: Chain A: Y.524, L.528, Q.573, F.576, W.577 Chain D: F.599, T.603, G.606, T.607, V.610, I.611 Ligands: PTY.1 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:V.610, D:I.611, D:I.611, A:Y.524, A:Y.524, A:L.528, A:F.576 Hydrogen bonds: D:T.607, A:Q.573 YZY.7: 12 residues within 4Å: Chain A: F.599, T.603, G.606, T.607, V.610, I.611 Chain B: Y.524, L.528, Q.573, F.576, W.577 Ligands: PTY.8 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.610, A:I.611, A:I.611, B:Y.524, B:Y.524, B:L.528, B:F.576 Hydrogen bonds: A:T.607, B:Q.573 YZY.13: 12 residues within 4Å: Chain B: F.599, T.603, G.606, T.607, V.610, I.611 Chain C: Y.524, L.528, Q.573, F.576, W.577 Ligands: PTY.14 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:V.610, B:I.611, B:I.611, C:Y.524, C:Y.524, C:L.528, C:F.576 Hydrogen bonds: B:T.607, C:Q.573 YZY.19: 12 residues within 4Å: Chain C: F.599, T.603, G.606, T.607, V.610, I.611 Chain D: Y.524, L.528, Q.573, F.576, W.577 Ligands: PTY.20 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.524, D:Y.524, D:L.528, D:F.576, C:V.610, C:I.611, C:I.611 Hydrogen bonds: D:Q.573, C:T.607

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Short transient receptor potential channel 5

Related Entries With Identical Sequence