SMTL ID : 9khk.1

Cryo-EM structure of homomeric TRPC channel, class 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 15 residues within 4Å: Chain A: H.432, D.433, W.434, W.435, M.438, A.441, I.484, I.487, L.488, Q.507, G.511 Chain B: T.603, M.604 Ligands: POV.2, YZY.7 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:T.603, A:M.438, A:A.441, A:I.484, A:I.487, A:L.488 Hydrogen bonds: A:H.432, A:D.433 PTY.8: 15 residues within 4Å: Chain B: H.432, D.433, W.434, W.435, M.438, A.441, I.484, I.487, L.488, Q.507, G.511 Chain D: T.603, M.604 Ligands: POV.9, YZY.19 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:M.438, B:A.441, B:I.484, B:I.487, B:L.488, D:T.603 Hydrogen bonds: B:H.432, B:D.433 PTY.13: 16 residues within 4Å: Chain A: T.603, M.604, I.611 Chain C: H.432, D.433, W.434, W.435, M.438, A.441, I.484, I.487, L.488, Q.507, G.511 Ligands: YZY.6, POV.14 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:M.438, C:A.441, C:I.484, C:I.487, C:L.488, A:T.603, A:I.611 Hydrogen bonds: C:H.432, C:D.433 PTY.20: 15 residues within 4Å: Chain C: T.603, M.604 Chain D: H.432, D.433, W.434, W.435, M.438, A.441, I.484, I.487, L.488, Q.507, G.511 Ligands: YZY.18, POV.21 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:M.438, D:A.441, D:I.484, D:I.487, D:L.488, C:T.603 Hydrogen bonds: D:H.432, D:D.433

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

POV.2: 6 residues within 4Å: Chain A: L.445, W.472, I.477, L.481, I.484 Ligands: PTY.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.445, A:L.481, A:I.484 Hydrogen bonds: A:W.472 POV.9: 6 residues within 4Å: Chain B: L.445, W.472, I.477, L.481, I.484 Ligands: PTY.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.445, B:L.481, B:I.484 Hydrogen bonds: B:W.472 POV.14: 6 residues within 4Å: Chain C: L.445, W.472, I.477, L.481, I.484 Ligands: PTY.13 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.445, C:L.481, C:I.484 Hydrogen bonds: C:W.472 POV.21: 6 residues within 4Å: Chain D: L.445, W.472, I.477, L.481, I.484 Ligands: PTY.20 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.445, 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: Y.316, F.367, T.371, L.375, L.493, L.496, F.497, A.499, N.500 Chain B: F.522, L.526 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.367, A:T.371, A:L.375, A:F.497, A:F.497, A:A.499, B:F.522, B:L.526 Hydrogen bonds: A:Y.316, A:N.500 Y01.10: 11 residues within 4Å: Chain B: Y.316, F.367, T.371, L.375, L.493, L.496, F.497, A.499, N.500 Chain D: F.522, L.526 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.367, B:T.371, B:L.375, B:F.497, B:F.497, B:A.499, D:F.522, D:L.526 Hydrogen bonds: B:Y.316, B:N.500 Y01.15: 11 residues within 4Å: Chain A: F.522, L.526 Chain C: Y.316, F.367, T.371, L.375, L.493, L.496, F.497, A.499, N.500 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.367, C:T.371, C:L.375, C:F.497, C:F.497, C:A.499, A:F.522, A:L.526 Hydrogen bonds: C:Y.316, C:N.500 Y01.22: 11 residues within 4Å: Chain C: F.522, L.526 Chain D: Y.316, F.367, T.371, L.375, L.493, L.496, F.497, A.499, N.500 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.367, D:T.371, D:L.375, D:F.497, D:F.497, D:A.499, C:F.522, C:L.526 Hydrogen bonds: 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.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.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 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.439 CA.12: 5 residues within 4Å: Chain B: E.418, E.421, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.439 CA.17: 5 residues within 4Å: Chain C: E.418, E.421, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.439 CA.24: 5 residues within 4Å: Chain D: E.418, E.421, N.436, D.439, R.492 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.439

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

YZY.6: 13 residues within 4Å: Chain A: F.599, A.602, T.603, G.606, T.607, V.610, I.611 Chain C: Y.524, L.572, Q.573, F.576, W.577 Ligands: PTY.13 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.524, C:L.572, C:Q.573, C:F.576, C:F.576, A:V.610, A:I.611 Hydrogen bonds: C:Q.573, A:T.607 YZY.7: 12 residues within 4Å: Chain A: Y.524, L.572, Q.573, F.576, W.577 Chain B: F.599, T.603, G.606, T.607, V.610, I.611 Ligands: PTY.1 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.610, B:I.611, A:Y.524, A:L.572, A:Q.573, A:F.576, A:F.576 Hydrogen bonds: B:T.607, A:Q.573 YZY.18: 12 residues within 4Å: Chain C: F.599, T.603, G.606, T.607, V.610, I.611 Chain D: Y.524, L.572, Q.573, F.576, W.577 Ligands: PTY.20 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.524, D:L.572, D:Q.573, D:F.576, D:F.576, C:V.610, C:I.611 Hydrogen bonds: D:Q.573, C:T.607 YZY.19: 12 residues within 4Å: Chain B: Y.524, L.572, Q.573, F.576, W.577 Chain D: F.599, T.603, G.606, T.607, V.610, I.611 Ligands: PTY.8 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:V.610, D:I.611, B:Y.524, B:L.572, 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 2. 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
B

C
D

D
C

Membrane

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

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