SMTL ID : 7dxf.1

Structure of BTDM-bound human TRPC6 nanodisc at 2.9 angstrom in high calcium state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.249, C.253, C.255, C.258 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.249, A:C.253, A:C.255, A:C.258 ZN.11: 4 residues within 4Å: Chain B: H.249, C.253, C.255, C.258 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.249, B:C.253, B:C.255, B:C.258 ZN.21: 4 residues within 4Å: Chain C: H.249, C.253, C.255, C.258 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.249, C:C.253, C:C.255, C:C.258 ZN.33: 4 residues within 4Å: Chain D: H.249, C.253, C.255, C.258 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.249, D:C.253, D:C.255, D:C.258

4 x W99: [2-(1,3-benzodioxol-5-ylamino)-1,3-thiazol-4-yl]-[(3R,5S)-3,5-dimethylpiperidin-1-yl]methanone(Non-covalent)

W99.2: 17 residues within 4Å: Chain A: F.607, S.608, I.610, A.611, Q.624, L.627, G.628, V.631 Chain D: I.640, M.643, V.644, A.647, F.648, T.714, L.719, M.722 Ligands: 98R.8 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:V.644, D:A.647, D:F.648, D:L.719, A:L.627, A:V.631 Hydrogen bonds: D:T.714, A:F.607 W99.12: 17 residues within 4Å: Chain A: I.640, M.643, V.644, A.647, F.648, T.714, L.719, M.722 Chain B: F.607, S.608, I.610, A.611, Q.624, L.627, G.628, V.631 Ligands: 98R.18 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.627, B:V.631, A:V.644, A:A.647, A:F.648, A:L.719 Hydrogen bonds: B:F.607, A:T.714 W99.22: 17 residues within 4Å: Chain B: I.640, M.643, V.644, A.647, F.648, T.714, L.719, M.722 Chain C: F.607, S.608, I.610, A.611, Q.624, L.627, G.628, V.631 Ligands: 98R.28 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:V.644, B:A.647, B:F.648, B:L.719, C:L.627, C:V.631 Hydrogen bonds: B:T.714, C:F.607 W99.34: 17 residues within 4Å: Chain C: I.640, M.643, V.644, A.647, F.648, T.714, L.719, M.722 Chain D: F.607, S.608, I.610, A.611, Q.624, L.627, G.628, V.631 Ligands: 98R.40 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.644, C:A.647, C:F.648, C:L.719, D:L.627, D:V.631 Hydrogen bonds: C:T.714, D:F.607

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 12 residues within 4Å: Chain A: Y.392, M.403, K.406, F.407, V.410, F.440, A.447, T.451, I.610, I.613, N.617 Ligands: POV.38 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.406, A:V.410, A:A.447, A:I.610, A:I.613 Y01.7: 6 residues within 4Å: Chain A: F.531, A.539, I.542, M.546, S.589, I.594 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.531, A:A.539, A:I.542 Hydrogen bonds: A:S.589 Y01.10: 9 residues within 4Å: Chain A: F.699, N.702, I.703, V.706 Chain B: I.536, I.601, L.605 Ligands: POV.16, 98R.18 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.536, B:I.601, B:L.605, A:F.699, A:F.699, A:N.702, A:V.706 Y01.13: 12 residues within 4Å: Chain B: Y.392, M.403, K.406, F.407, V.410, F.440, A.447, T.451, I.610, I.613, N.617 Ligands: POV.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.406, B:V.410, B:A.447, B:I.610, B:I.613 Y01.17: 6 residues within 4Å: Chain B: F.531, A.539, I.542, M.546, S.589, I.594 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.531, B:A.539, B:I.542 Hydrogen bonds: B:S.589 Y01.20: 9 residues within 4Å: Chain B: F.699, N.702, I.703, V.706 Chain C: I.536, I.601, L.605 Ligands: POV.26, 98R.28 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.536, C:I.601, C:L.605, B:F.699, B:F.699, B:N.702, B:V.706 Y01.23: 12 residues within 4Å: Chain C: Y.392, M.403, K.406, F.407, V.410, F.440, A.447, T.451, I.610, I.613, N.617 Ligands: POV.16 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.406, C:V.410, C:A.447, C:I.610, C:I.613 Y01.27: 6 residues within 4Å: Chain C: F.531, A.539, I.542, M.546, S.589, I.594 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.531, C:A.539, C:I.542 Hydrogen bonds: C:S.589 Y01.30: 9 residues within 4Å: Chain C: F.699, N.702, I.703, V.706 Chain D: I.536, I.601, L.605 Ligands: POV.38, 98R.40 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.536, D:I.601, D:L.605, C:F.699, C:F.699, C:N.702, C:V.706 Y01.32: 9 residues within 4Å: Chain A: I.536, I.601, L.605 Chain D: F.699, N.702, I.703, V.706 Ligands: POV.6, 98R.8 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.699, D:F.699, D:N.702, D:V.706, A:I.536, A:I.601, A:L.605 Y01.35: 12 residues within 4Å: Chain D: Y.392, M.403, K.406, F.407, V.410, F.440, A.447, T.451, I.610, I.613, N.617 Ligands: POV.26 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:K.406, D:V.410, D:A.447, D:I.610, D:I.613 Y01.39: 6 residues within 4Å: Chain D: F.531, A.539, I.542, M.546, S.589, I.594 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.531, D:A.539, D:I.542 Hydrogen bonds: D:S.589

12 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: E.144, D.890 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.144, A:E.144, A:D.890 CA.5: 3 residues within 4Å: Chain A: E.509, E.512, N.527 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.509, A:E.509, A:E.512 CA.9: 4 residues within 4Å: Chain A: E.881 Chain B: E.878, N.880, E.883 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.878, B:E.883, A:E.881 CA.14: 2 residues within 4Å: Chain B: E.144, D.890 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.144, B:E.144, B:D.890 CA.15: 3 residues within 4Å: Chain B: E.509, E.512, N.527 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.509, B:E.509, B:E.512 CA.19: 4 residues within 4Å: Chain B: E.881 Chain C: E.878, N.880, E.883 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:E.878, C:E.883, B:E.881 CA.24: 2 residues within 4Å: Chain C: E.144, D.890 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.144, C:E.144, C:D.890 CA.25: 3 residues within 4Å: Chain C: E.509, E.512, N.527 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.509, C:E.509, C:E.512 CA.29: 4 residues within 4Å: Chain C: E.881 Chain D: E.878, N.880, E.883 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:E.878, D:E.883, C:E.881 CA.31: 4 residues within 4Å: Chain A: E.878, N.880, E.883 Chain D: E.881 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Metal complexes: D:E.881, A:E.878, A:E.883 CA.36: 2 residues within 4Å: Chain D: E.144, D.890 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.144, D:E.144, D:D.890 CA.37: 3 residues within 4Å: Chain D: E.509, E.512, N.527 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.509, D:E.509, D:E.512

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

POV.6: 15 residues within 4Å: Chain A: M.638, I.642, F.645, V.646, M.649, V.671, E.672, F.675 Chain B: V.458, F.465 Chain D: N.702, I.717 Ligands: 98R.8, Y01.13, Y01.32 13 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: A:I.642, A:F.645, A:F.645, A:V.646, A:V.646, A:V.671, A:F.675, A:F.675, D:I.717, B:V.458, B:F.465, B:F.465 Salt bridges: A:E.672 POV.16: 15 residues within 4Å: Chain A: N.702, I.717 Chain B: M.638, I.642, F.645, V.646, M.649, V.671, E.672, F.675 Chain C: V.458, F.465 Ligands: Y01.10, 98R.18, Y01.23 13 PLIP interactions: 9 interactions with chain B, 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:I.642, B:F.645, B:F.645, B:V.646, B:V.646, B:V.671, B:F.675, B:F.675, C:V.458, C:F.465, C:F.465, A:I.717 Salt bridges: B:E.672 POV.26: 15 residues within 4Å: Chain B: N.702, I.717 Chain C: M.638, I.642, F.645, V.646, M.649, V.671, E.672, F.675 Chain D: V.458, F.465 Ligands: Y01.20, 98R.28, Y01.35 13 PLIP interactions: 1 interactions with chain B, 9 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: B:I.717, C:I.642, C:F.645, C:F.645, C:V.646, C:V.646, C:V.671, C:F.675, C:F.675, D:V.458, D:F.465, D:F.465 Salt bridges: C:E.672 POV.38: 15 residues within 4Å: Chain A: V.458, F.465 Chain C: N.702, I.717 Chain D: M.638, I.642, F.645, V.646, M.649, V.671, E.672, F.675 Ligands: Y01.3, Y01.30, 98R.40 13 PLIP interactions: 9 interactions with chain D, 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: D:I.642, D:F.645, D:F.645, D:V.646, D:V.646, D:V.671, D:F.675, D:F.675, A:V.458, A:F.465, A:F.465, C:I.717 Salt bridges: D:E.672

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

98R.8: 16 residues within 4Å: Chain A: V.631, I.642, E.672, F.675, K.676, F.679, W.680 Chain D: N.702, Y.705, G.709, V.710, V.713, T.714 Ligands: W99.2, POV.6, Y01.32 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.631, A:I.642, A:F.675, A:F.679, A:F.679, A:F.679, D:V.713 Hydrogen bonds: A:E.672 Salt bridges: A:K.676 98R.18: 16 residues within 4Å: Chain A: N.702, Y.705, G.709, V.710, V.713, T.714 Chain B: V.631, I.642, E.672, F.675, K.676, F.679, W.680 Ligands: Y01.10, W99.12, POV.16 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:V.713, B:V.631, B:I.642, B:F.675, B:F.679, B:F.679, B:F.679 Hydrogen bonds: B:E.672 Salt bridges: B:K.676 98R.28: 16 residues within 4Å: Chain B: N.702, Y.705, G.709, V.710, V.713, T.714 Chain C: V.631, I.642, E.672, F.675, K.676, F.679, W.680 Ligands: Y01.20, W99.22, POV.26 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.631, C:I.642, C:F.675, C:F.679, C:F.679, C:F.679, B:V.713 Hydrogen bonds: C:E.672 Salt bridges: C:K.676 98R.40: 16 residues within 4Å: Chain C: N.702, Y.705, G.709, V.710, V.713, T.714 Chain D: V.631, I.642, E.672, F.675, K.676, F.679, W.680 Ligands: Y01.30, W99.34, POV.38 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.631, D:I.642, D:F.675, D:F.679, D:F.679, D:F.679, C:V.713 Hydrogen bonds: D:E.672 Salt bridges: D:K.676

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 6: 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 6

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