SMTL ID : 7x6c.1

Cryo-EM structure of the human TRPC5 ion channel in lipid nanodiscs, class1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 17 residues within 4Å: Chain A: D.433, W.434, W.435, M.438, A.441, I.484, I.487, L.488, L.491, Q.507, L.510, L.514 Chain D: T.603, M.604, T.607 Ligands: POV.2, YZY.19 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.435, A:M.438, A:A.441, A:I.484, A:I.487, A:L.488, A:L.491, A:L.514, D:T.603, D:T.607 Hydrogen bonds: A:D.433, A:Q.507 PTY.7: 17 residues within 4Å: Chain B: D.433, W.434, W.435, M.438, A.441, I.484, I.487, L.488, L.491, Q.507, L.510, L.514 Chain C: T.603, M.604, T.607 Ligands: POV.8, YZY.13 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.435, B:M.438, B:A.441, B:I.484, B:I.487, B:L.488, B:L.491, B:L.514, C:T.603, C:T.607 Hydrogen bonds: B:D.433, B:Q.507 PTY.14: 17 residues within 4Å: Chain A: T.603, M.604, T.607 Chain C: D.433, W.434, W.435, M.438, A.441, I.484, I.487, L.488, L.491, Q.507, L.510, L.514 Ligands: YZY.6, POV.15 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.435, C:M.438, C:A.441, C:I.484, C:I.487, C:L.488, C:L.491, C:L.514, A:T.603, A:T.607 Hydrogen bonds: C:D.433, C:Q.507 PTY.20: 17 residues within 4Å: Chain B: T.603, M.604, T.607 Chain D: D.433, W.434, W.435, M.438, A.441, I.484, I.487, L.488, L.491, Q.507, L.510, L.514 Ligands: YZY.12, POV.21 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain D Hydrophobic interactions: B:T.603, B:T.607, D:W.435, D:M.438, D:A.441, D:I.484, D:I.487, D:L.488, D:L.491, D:L.514 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, L.452, W.472, I.477 Ligands: PTY.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.445, A:A.448, A:L.452 Hydrogen bonds: A:W.472 POV.8: 8 residues within 4Å: Chain B: S.444, L.445, A.448, L.452, W.472, I.477, I.484 Ligands: PTY.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.445, B:A.448, B:L.452, B:I.484 Hydrogen bonds: B:W.472 POV.15: 7 residues within 4Å: Chain C: S.444, L.445, A.448, L.452, W.472, I.477 Ligands: PTY.14 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.445, C:A.448, C:L.452 Hydrogen bonds: C:W.472 POV.21: 7 residues within 4Å: Chain D: S.444, L.445, A.448, L.452, W.472, I.477 Ligands: PTY.20 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.445, D:A.448, D:L.452 Hydrogen bonds: D:W.472

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 11 residues within 4Å: Chain A: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499 Chain D: C.525, L.529 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.364, A:T.371, A:L.375, A:L.493, A:F.497, A:F.497, A:A.499, D:L.529 Hydrogen bonds: A:W.315, A:Y.316 Y01.9: 11 residues within 4Å: Chain B: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499 Chain C: C.525, L.529 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.364, B:T.371, B:L.375, B:L.493, B:F.497, B:F.497, B:A.499, C:L.529 Hydrogen bonds: B:W.315, B:Y.316 Y01.16: 11 residues within 4Å: Chain A: C.525, L.529 Chain C: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.364, C:T.371, C:L.375, C:L.493, C:F.497, C:F.497, C:A.499, A:L.529 Hydrogen bonds: C:W.315, C:Y.316 Y01.22: 11 residues within 4Å: Chain B: C.525, L.529 Chain D: W.315, Y.316, F.364, T.371, L.375, L.493, L.496, F.497, A.499 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.364, D:T.371, D:L.375, D:L.493, D:F.497, D:F.497, D:A.499, B:L.529 Hydrogen bonds: D:W.315, D:Y.316

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.10: 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: 4 residues within 4Å: Chain A: E.418, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.418, A:D.439 CA.11: 4 residues within 4Å: Chain B: E.418, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.418, B:D.439 CA.18: 4 residues within 4Å: Chain C: E.418, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.418, C:D.439 CA.24: 4 residues within 4Å: Chain D: E.418, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.418, D:D.439

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

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.14 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:T.607, A:V.610, A:V.610, A:I.611, C:L.514, C:L.514, C:L.521, C:Y.524, C:L.528, C:F.576, C:F.576, C:F.576 Hydrogen bonds: A:T.607, C:Q.573 YZY.12: 14 residues within 4Å: Chain B: 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.20 14 PLIP interactions: 9 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:L.514, D:L.514, D:L.521, D:Y.524, D:L.528, D:F.576, D:F.576, D:F.576, B:T.607, B:V.610, B:V.610, B:I.611 Hydrogen bonds: D:Q.573, B:T.607 YZY.13: 15 residues within 4Å: Chain B: L.514, L.521, Y.524, C.525, L.528, Q.573, F.576, W.577 Chain C: F.599, T.603, G.606, T.607, V.610, I.611 Ligands: PTY.7 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:L.514, B:L.514, B:L.521, B:Y.524, B:L.528, B:F.576, B:F.576, B:F.576, C:T.607, C:V.610, C:V.610, C:I.611, C:I.611 Hydrogen bonds: B:Q.573, C:T.607 YZY.19: 15 residues within 4Å: Chain A: L.514, L.521, Y.524, C.525, 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 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:L.514, A:L.514, A:L.521, A:Y.524, A:L.528, A:F.576, A:F.576, A:F.576, D:T.607, D:V.610, D:V.610, D:I.611, D:I.611 Hydrogen bonds: A:Q.573, D: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
C

B
A

C
B

D
D

Membrane

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

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