SMTL ID : 6aei.1

Cryo-EM structure of the receptor-activated TRPC5 ion channel

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

5 x NA: SODIUM ION(Non-functional Binders)

NA.1: 1 residues within 4Å: Chain A: G.581 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.581 NA.2: 4 residues within 4Å: Chain A: E.418, E.421, N.436, D.439 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.418 NA.5: 4 residues within 4Å: Chain B: E.418, E.421, N.436, D.439 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.421 NA.8: 4 residues within 4Å: Chain C: E.418, E.421, N.436, D.439 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.418 NA.11: 4 residues within 4Å: Chain D: E.418, E.421, N.436, D.439 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.421

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 15 residues within 4Å: Chain A: W.315, Y.316, W.322, F.364, L.375, L.493, L.496, F.497, A.499, N.500, W.647 Chain D: F.522, C.525, L.526, L.529 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:F.364, A:L.375, A:L.493, A:L.496, A:F.497, A:F.497, D:F.522, D:F.522, D:F.522, D:L.526, D:L.529 Hydrogen bonds: A:W.647 Y01.6: 12 residues within 4Å: Chain A: F.522, L.526, L.529 Chain B: W.315, Y.316, W.322, F.364, L.375, L.496, F.497, A.499, N.500 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.522, A:F.522, A:F.522, A:L.526, A:L.529, B:W.322, B:F.364, B:L.375, B:L.496, B:F.497, B:F.497 Y01.9: 15 residues within 4Å: Chain B: F.522, C.525, L.526, L.529 Chain C: W.315, Y.316, W.322, F.364, L.375, L.493, L.496, F.497, A.499, N.500, W.647 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:F.522, B:F.522, B:F.522, B:L.526, B:L.529, C:W.322, C:F.364, C:L.375, C:L.493, C:L.496, C:F.497, C:F.497 Hydrogen bonds: C:W.647 Y01.12: 12 residues within 4Å: Chain C: F.522, L.526, L.529 Chain D: W.315, Y.316, W.322, F.364, L.375, L.496, F.497, A.499, N.500 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.364, D:L.375, D:L.496, D:F.497, D:F.497, C:F.522, C:F.522, C:F.522, C:L.526, C:L.529

4 x LPP: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE(Non-covalent)

LPP.4: 20 residues within 4Å: Chain A: L.514, L.521, Y.524, C.525, L.528, R.557, L.572, Q.573, F.576, W.577, V.579, S.612 Chain D: F.599, A.602, T.603, T.607, V.610, I.611, V.614, V.615 16 PLIP interactions: 7 interactions with chain D, 9 interactions with chain A Hydrophobic interactions: D:T.607, D:V.610, D:I.611, D:I.611, D:V.614, D:V.615, D:V.615, A:L.514, A:L.521, A:Y.524, A:Q.573, A:F.576, A:F.576, A:V.579 Hydrogen bonds: A:R.557, A:Q.573 LPP.7: 22 residues within 4Å: Chain A: F.599, A.602, T.603, G.606, T.607, V.610, I.611, V.614 Chain B: L.510, L.514, L.521, Y.524, C.525, L.528, R.557, L.572, Q.573, F.576, W.577, V.579, S.612, L.617 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.510, B:L.514, B:L.521, B:Y.524, B:L.528, B:Q.573, B:F.576, B:F.576, B:V.579, B:L.617, A:T.607, A:I.611, A:I.611, A:V.614, A:V.614 Hydrogen bonds: B:R.557, B:Q.573, B:Q.573 LPP.10: 22 residues within 4Å: Chain B: F.599, A.602, T.603, T.607, V.610, I.611, V.614, V.615 Chain C: L.510, L.514, L.521, Y.524, C.525, R.557, F.569, L.572, Q.573, F.576, W.577, V.579, S.612, L.617 19 PLIP interactions: 11 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:L.510, C:L.514, C:L.521, C:Y.524, C:F.569, C:Q.573, C:F.576, C:V.579, C:L.617, B:T.607, B:V.610, B:V.610, B:I.611, B:I.611, B:V.614, B:V.615, B:V.615 Hydrogen bonds: C:R.557, C:Q.573 LPP.13: 20 residues within 4Å: Chain C: F.599, A.602, T.603, T.607, V.610, I.611, V.614, V.615 Chain D: L.510, L.514, L.521, Y.524, R.557, L.572, Q.573, F.576, W.577, V.579, S.612, L.617 17 PLIP interactions: 11 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:L.510, D:L.514, D:L.521, D:Q.573, D:F.576, D:F.576, D:V.579, D:L.617, C:T.607, C:I.611, C:I.611, C:V.614, C:V.614, C:V.615 Hydrogen bonds: D:R.557, D:Q.573, D:Q.573

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, J. et al., Cryo-EM structure of TRPC5 at 2.8- angstrom resolution reveals unique and conserved structural elements essential for channel function. Sci Adv (2019)

Release Date

2019-08-07

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.
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Short transient receptor potential channel 5