SMTL ID : 9khj.1

Cryo-EM structure of homomeric TRPC channel, class 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.62 Å

Oligo State

homo-tetramer

Ligands

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 16 residues within 4Å: Chain A: D.433, W.434, W.435, M.438, I.484, I.487, L.488, L.491, I.494, Q.507, G.511, L.514 Chain C: T.603, M.604, T.607 Ligands: YZY.18 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.435, A:M.438, A:I.484, A:I.487, A:L.488, A:L.491, A:I.494, A:L.514, C:T.603 Hydrogen bonds: A:Q.507 PTY.7: 16 residues within 4Å: Chain B: D.433, W.434, W.435, M.438, I.484, I.487, L.488, L.491, I.494, Q.507, G.511, L.514 Chain D: T.603, M.604, T.607 Ligands: YZY.24 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:W.435, B:M.438, B:I.484, B:I.487, B:L.488, B:I.494, B:L.514, D:T.603 Hydrogen bonds: B:Q.507 PTY.13: 16 residues within 4Å: Chain B: T.603, M.604, T.607 Chain C: D.433, W.434, W.435, M.438, I.484, I.487, L.488, L.491, I.494, Q.507, G.511, L.514 Ligands: YZY.12 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.435, C:M.438, C:I.484, C:I.487, C:L.488, C:I.494, C:L.514, B:T.603 Hydrogen bonds: C:Q.507 PTY.19: 16 residues within 4Å: Chain A: T.603, M.604, T.607 Chain D: D.433, W.434, W.435, M.438, I.484, I.487, L.488, L.491, I.494, Q.507, G.511, L.514 Ligands: YZY.6 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.435, D:M.438, D:I.484, D:I.487, D:L.488, D:L.491, D:I.494, D:L.514, A:T.603 Hydrogen bonds: D:Q.507

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

POV.2: 8 residues within 4Å: Chain A: A.441, S.444, L.445, A.448, L.452, W.472, L.481, I.484 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.441, A:L.445, A:A.448, A:L.452, A:L.481, A:I.484 Hydrogen bonds: A:W.472 POV.8: 8 residues within 4Å: Chain B: A.441, S.444, L.445, A.448, L.452, W.472, L.481, I.484 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.441, B:L.445, B:A.448, B:L.452, B:L.481, B:I.484 Hydrogen bonds: B:W.472 POV.14: 8 residues within 4Å: Chain C: A.441, S.444, L.445, A.448, L.452, W.472, L.481, I.484 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.441, C:L.445, C:A.448, C:L.452, C:L.481, C:I.484 Hydrogen bonds: C:W.472 POV.20: 8 residues within 4Å: Chain D: A.441, S.444, L.445, A.448, L.452, W.472, L.481, I.484 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.441, D:L.445, D:A.448, D:L.452, D:L.481, D:I.484 Hydrogen bonds: D:W.472

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 11 residues within 4Å: Chain A: T.371, L.375, L.493, L.496, F.497, A.499, N.500, S.501 Chain C: F.522, C.525, L.526 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.371, A:L.493, A:F.497, A:F.497, A:A.499 Hydrogen bonds: A:N.500, A:S.501 Y01.9: 11 residues within 4Å: Chain B: T.371, L.375, L.493, L.496, F.497, A.499, N.500, S.501 Chain D: F.522, C.525, L.526 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:T.371, B:L.493, B:F.497, B:F.497, B:A.499, D:L.526 Hydrogen bonds: B:N.500, B:S.501 Y01.15: 11 residues within 4Å: Chain B: F.522, C.525, L.526 Chain C: T.371, L.375, L.493, L.496, F.497, A.499, N.500, S.501 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:T.371, C:L.493, C:F.497, C:F.497, C:A.499 Hydrogen bonds: C:N.500, C:S.501 Y01.21: 11 residues within 4Å: Chain A: F.522, C.525, L.526 Chain D: T.371, L.375, L.493, L.496, F.497, A.499, N.500, S.501 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:T.371, D:L.493, D:F.497, D:F.497, D:A.499, A:L.526 Hydrogen bonds: D:N.500, D:S.501

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.16: 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.22: 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, E.421, N.436, D.439 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.418, A:E.418, A:D.439 CA.11: 4 residues within 4Å: Chain B: E.418, E.421, N.436, D.439 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.418, B:E.418, B:D.439 CA.17: 4 residues within 4Å: Chain C: E.418, E.421, N.436, D.439 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.418, C:E.418, C:D.439 CA.23: 4 residues within 4Å: Chain D: E.418, E.421, N.436, D.439 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.418, D:E.418, 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: F.599, A.602, T.603, G.606, T.607, I.611 Chain D: L.514, Y.524, Q.573, F.576, W.577 Ligands: PTY.19 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:I.611, A:I.611, D:L.514, D:Y.524, D:Q.573, D:F.576, D:F.576 Hydrogen bonds: A:T.607, D:Q.573 YZY.12: 12 residues within 4Å: Chain B: F.599, A.602, T.603, G.606, T.607, I.611 Chain C: L.514, Y.524, Q.573, F.576, W.577 Ligands: PTY.13 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:I.611, B:I.611, C:L.514, C:Y.524, C:Q.573, C:F.576, C:F.576 Hydrogen bonds: B:T.607, C:Q.573 YZY.18: 12 residues within 4Å: Chain A: L.514, Y.524, Q.573, F.576, W.577 Chain C: F.599, A.602, T.603, G.606, T.607, I.611 Ligands: PTY.1 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.514, A:Y.524, A:Q.573, A:F.576, A:F.576, C:I.611, C:I.611 Hydrogen bonds: A:Q.573, C:T.607 YZY.24: 12 residues within 4Å: Chain B: L.514, Y.524, Q.573, F.576, W.577 Chain D: F.599, A.602, T.603, G.606, T.607, I.611 Ligands: PTY.7 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:I.611, D:I.611, B:L.514, B:Y.524, B:Q.573, B:F.576, B:F.576 Hydrogen bonds: D:T.607, B:Q.573

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S.-H. et al., Cryo-EM structure of homomeric TRPC channel, class 1. To Be Published

Release Date

2025-11-12

Peptides

Short transient receptor potential channel 5: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

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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