SMTL ID : 7dxb.1

Structure of TRPC3 at 2.7 angstrom in high calcium state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 17 residues within 4Å: Chain A: S.466, S.520, I.525, L.529, I.532, V.535, L.536, E.603 Chain B: K.629, F.630, N.633, I.634, V.637, I.641, T.645 Ligands: Y01.3, 98R.10 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.525, A:I.525, A:L.529, A:I.532, A:I.532, A:L.536, B:F.630, B:F.630, B:I.634, B:V.637 Hydrogen bonds: B:N.633 POV.8: 17 residues within 4Å: Chain A: K.629, F.630, N.633, I.634, V.637, I.641, T.645 Chain D: S.466, S.520, I.525, L.529, I.532, V.535, L.536, E.603 Ligands: 98R.9, Y01.28 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:F.630, A:F.630, A:I.634, A:V.637, D:I.525, D:I.525, D:L.529, D:I.532, D:I.532, D:L.536 Hydrogen bonds: A:N.633 POV.11: 17 residues within 4Å: Chain B: S.466, S.520, I.525, L.529, I.532, V.535, L.536, E.603 Chain C: K.629, F.630, N.633, I.634, V.637, I.641, T.645 Ligands: Y01.13, 98R.18 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:I.525, B:I.525, B:L.529, B:I.532, B:I.532, B:L.536, C:F.630, C:F.630, C:I.634, C:V.637 Hydrogen bonds: C:N.633 POV.19: 17 residues within 4Å: Chain C: S.466, S.520, I.525, L.529, I.532, V.535, L.536, E.603 Chain D: K.629, F.630, N.633, I.634, V.637, I.641, T.645 Ligands: Y01.21, 98R.26 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:F.630, D:F.630, D:I.634, D:V.637, C:I.525, C:I.525, C:L.529, C:I.532, C:I.532, C:L.536 Hydrogen bonds: D:N.633

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 11 residues within 4Å: Chain A: W.322, Y.323, K.337, V.341, F.371, F.374, I.382, I.544, A.547, N.548, E.549 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.337, A:V.341, A:I.382, A:I.544, A:A.547, A:N.548 Hydrogen bonds: A:Y.323, A:N.548 Salt bridges: A:K.337 Y01.3: 10 residues within 4Å: Chain A: M.437, A.470, T.473, A.474, L.477, Q.481, S.520, P.522, I.525 Ligands: POV.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.470, A:T.473, A:A.474, A:L.477, A:I.525 Hydrogen bonds: A:Q.481 Y01.12: 11 residues within 4Å: Chain B: W.322, Y.323, K.337, V.341, F.371, F.374, I.382, I.544, A.547, N.548, E.549 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:K.337, B:V.341, B:I.382, B:I.544, B:A.547, B:N.548 Hydrogen bonds: B:Y.323, B:N.548 Salt bridges: B:K.337 Y01.13: 10 residues within 4Å: Chain B: M.437, A.470, T.473, A.474, L.477, Q.481, S.520, P.522, I.525 Ligands: POV.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.470, B:T.473, B:A.474, B:L.477, B:I.525 Hydrogen bonds: B:Q.481 Y01.20: 11 residues within 4Å: Chain C: W.322, Y.323, K.337, V.341, F.371, F.374, I.382, I.544, A.547, N.548, E.549 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:K.337, C:V.341, C:I.382, C:I.544, C:A.547, C:N.548 Hydrogen bonds: C:Y.323, C:N.548 Salt bridges: C:K.337 Y01.21: 10 residues within 4Å: Chain C: M.437, A.470, T.473, A.474, L.477, Q.481, S.520, P.522, I.525 Ligands: POV.19 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.470, C:T.473, C:A.474, C:L.477, C:I.525 Hydrogen bonds: C:Q.481 Y01.27: 11 residues within 4Å: Chain D: W.322, Y.323, K.337, V.341, F.371, F.374, I.382, I.544, A.547, N.548, E.549 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:K.337, D:V.341, D:I.382, D:I.544, D:A.547, D:N.548 Hydrogen bonds: D:Y.323, D:N.548 Salt bridges: D:K.337 Y01.28: 10 residues within 4Å: Chain D: M.437, A.470, T.473, A.474, L.477, Q.481, S.520, P.522, I.525 Ligands: POV.8 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.470, D:T.473, D:A.474, D:L.477, D:I.525 Hydrogen bonds: D:Q.481

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.178, C.182, C.184, C.187 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.178, A:C.182, A:C.184, A:C.187 ZN.14: 4 residues within 4Å: Chain B: H.178, C.182, C.184, C.187 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.178, B:C.182, B:C.184, B:C.187 ZN.22: 4 residues within 4Å: Chain C: H.178, C.182, C.184, C.187 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.178, C:C.182, C:C.184, C:C.187 ZN.29: 4 residues within 4Å: Chain D: H.178, C.182, C.184, C.187 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.178, D:C.182, D:C.184, D:C.187

12 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: E.73, D.798 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.73, A:E.73, A:D.798 CA.6: 4 residues within 4Å: Chain A: E.786, N.788, E.791 Chain B: E.789 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.786, A:E.791, B:E.789 CA.7: 3 residues within 4Å: Chain A: E.440, E.443, N.458 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.440, A:E.443 CA.15: 2 residues within 4Å: Chain B: E.73, D.798 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.73, B:E.73, B:D.798 CA.16: 4 residues within 4Å: Chain B: E.786, N.788, E.791 Chain C: E.789 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Metal complexes: B:E.786, B:E.791, C:E.789 CA.17: 3 residues within 4Å: Chain B: E.440, E.443, N.458 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.440, B:E.443 CA.23: 2 residues within 4Å: Chain C: E.73, D.798 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.73, C:E.73, C:D.798 CA.24: 4 residues within 4Å: Chain C: E.786, N.788, E.791 Chain D: E.789 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Metal complexes: C:E.786, C:E.791, D:E.789 CA.25: 3 residues within 4Å: Chain C: E.440, E.443, N.458 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.440, C:E.443 CA.30: 2 residues within 4Å: Chain D: E.73, D.798 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.73, D:E.73, D:D.798 CA.31: 4 residues within 4Å: Chain A: E.789 Chain D: E.786, N.788, E.791 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Metal complexes: A:E.789, D:E.786, D:E.791 CA.32: 3 residues within 4Å: Chain D: E.440, E.443, N.458 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.440, D:E.443

4 x 98R: [(2S)-2-[(E)-octadec-10-enoyl]oxy-3-oxidanyl-propyl] octadec-10-enoate(Non-covalent)

98R.9: 13 residues within 4Å: Chain A: N.633, Y.636, V.637, G.640, I.641, V.644, T.645 Chain D: E.603, F.606, K.607, F.610, W.611 Ligands: POV.8 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:V.644, A:V.644, A:T.645, D:F.606, D:F.606, D:F.610, D:F.610 Hydrogen bonds: A:N.633, D:E.603 98R.10: 13 residues within 4Å: Chain A: E.603, F.606, K.607, F.610, W.611 Chain B: N.633, Y.636, V.637, G.640, I.641, V.644, T.645 Ligands: POV.1 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.644, B:V.644, B:T.645, A:F.606, A:F.606, A:F.610, A:F.610 Hydrogen bonds: B:N.633, A:E.603 98R.18: 13 residues within 4Å: Chain B: E.603, F.606, K.607, F.610, W.611 Chain C: N.633, Y.636, V.637, G.640, I.641, V.644, T.645 Ligands: POV.11 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.606, B:F.606, B:F.610, B:F.610, C:V.644, C:V.644, C:T.645 Hydrogen bonds: B:E.603, C:N.633 98R.26: 13 residues within 4Å: Chain C: E.603, F.606, K.607, F.610, W.611 Chain D: N.633, Y.636, V.637, G.640, I.641, V.644, T.645 Ligands: POV.19 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.644, D:V.644, D:T.645, C:F.606, C:F.606, C:F.610, C:F.610 Hydrogen bonds: D:N.633, C:E.603

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, W. et al., Structural mechanism of human TRPC3 and TRPC6 channel regulation by their intracellular calcium-binding sites. Neuron (2022)

Release Date

2022-02-02

Peptides

Short transient receptor potential channel 3: 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 3

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