SMTL ID : 9cuh.1

Structure of human full-length ancestral TRPV6 channel in apo open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 15 residues within 4Å: Chain A: L.372, I.375, Y.376, Y.379, V.431, I.434, G.435, I.438, E.443, G.463, F.465, H.466, Y.507, R.510 Ligands: POV.10 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.372, A:Y.376, A:Y.379, A:I.434, A:I.438, A:F.465, A:Y.507, A:Y.507 Hydrogen bonds: A:G.463 Salt bridges: A:H.466, A:H.466, A:R.510, A:K.647 Y01.2: 18 residues within 4Å: Chain A: P.464, F.465, S.495, F.496, V.499, C.503, M.506, R.510, T.519, I.520, Q.523, I.526, F.527, Q.636 Chain B: I.597, T.598, I.605 Ligands: POV.6 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:I.597, B:I.605, A:P.464, A:F.496, A:I.526, A:F.527 Hydrogen bonds: A:T.519, A:Q.636 Water bridges: A:R.510 Salt bridges: A:R.510 Y01.11: 12 residues within 4Å: Chain A: L.591, F.593, S.596, A.600, I.604 Chain D: C.534, M.537, P.567, L.570, F.571, F.574 Ligands: POV.12 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.593, A:A.600, A:I.604, D:L.570, D:F.571, D:F.574 Hydrogen bonds: A:L.591 Y01.14: 12 residues within 4Å: Chain A: C.534, M.537, P.567, L.570, F.571, F.574 Chain B: L.591, F.593, S.596, A.600, I.604 Ligands: POV.15 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.570, A:F.574, B:F.593, B:A.600, B:I.604 Hydrogen bonds: B:L.591 Y01.16: 15 residues within 4Å: Chain B: L.372, I.375, Y.376, Y.379, V.431, I.434, G.435, I.438, E.443, G.463, F.465, H.466, Y.507, R.510 Ligands: POV.25 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.372, B:Y.376, B:Y.379, B:I.434, B:I.438, B:F.465, B:Y.507, B:Y.507 Hydrogen bonds: B:G.463 Salt bridges: B:H.466, B:H.466, B:R.510, B:K.647 Y01.17: 18 residues within 4Å: Chain B: P.464, F.465, S.495, F.496, V.499, C.503, M.506, R.510, T.519, I.520, Q.523, I.526, Q.636 Chain C: I.597, T.598, I.605 Ligands: POV.21, POV.27 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.464, B:F.496, B:I.526, C:I.597, C:I.605 Hydrogen bonds: B:T.519, B:Q.636 Water bridges: B:R.510 Salt bridges: B:R.510 Y01.26: 12 residues within 4Å: Chain B: C.534, M.537, P.567, L.570, F.571, F.574 Chain C: L.591, F.593, S.596, A.600, I.604 Ligands: POV.27 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.593, C:A.600, C:I.604, B:L.570, B:F.571, B:F.574 Hydrogen bonds: C:L.591 Y01.28: 15 residues within 4Å: Chain C: L.372, I.375, Y.376, Y.379, V.431, I.434, G.435, I.438, E.443, G.463, F.465, H.466, Y.507, R.510 Ligands: POV.37 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.372, C:Y.376, C:Y.379, C:I.434, C:I.438, C:F.465, C:Y.507, C:Y.507 Hydrogen bonds: C:G.463 Salt bridges: C:H.466, C:H.466, C:R.510, C:K.647 Y01.29: 18 residues within 4Å: Chain C: P.464, F.465, S.495, F.496, V.499, C.503, M.506, R.510, T.519, I.520, Q.523, I.526, Q.636 Chain D: I.597, T.598, I.605 Ligands: POV.33, POV.41 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:I.597, D:I.605, C:P.464, C:F.496, C:V.499, C:I.526 Hydrogen bonds: C:T.519, C:Q.636 Water bridges: C:R.510 Salt bridges: C:R.510 Y01.40: 12 residues within 4Å: Chain C: C.534, M.537, P.567, L.570, F.571, F.574 Chain D: L.591, F.593, S.596, A.600, I.604 Ligands: POV.41 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.570, C:F.571, C:F.574, D:F.593, D:A.600, D:I.604 Hydrogen bonds: D:L.591 Y01.42: 16 residues within 4Å: Chain D: L.372, I.375, Y.376, Y.379, V.431, I.434, G.435, I.438, V.442, E.443, G.463, F.465, H.466, Y.507, R.510 Ligands: POV.39 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.372, D:Y.376, D:Y.379, D:I.434, D:I.438, D:V.442, D:F.465, D:Y.507, D:Y.507 Hydrogen bonds: D:G.463 Salt bridges: D:H.466, D:H.466, D:R.510, D:K.647 Y01.43: 17 residues within 4Å: Chain A: I.597, T.598, I.605 Chain D: P.464, F.465, S.495, F.496, V.499, C.503, M.506, R.510, T.519, Q.523, I.526, Q.636 Ligands: POV.12, POV.47 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:P.464, D:F.496, D:F.496, D:V.499, D:I.526, A:I.597, A:I.605 Hydrogen bonds: D:T.519, D:Q.636 Water bridges: D:R.510 Salt bridges: D:R.510

4 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.3: 4 residues within 4Å: Chain D: L.515 Ligands: POV.5, POV.38, POV.39 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.515 PCW.18: 4 residues within 4Å: Chain A: L.515 Ligands: POV.9, POV.10, POV.20 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.515 PCW.30: 4 residues within 4Å: Chain B: L.515 Ligands: POV.24, POV.25, POV.32 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.515 PCW.44: 4 residues within 4Å: Chain C: L.515 Ligands: POV.36, POV.37, POV.46 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.515

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

POV.4: 8 residues within 4Å: Chain A: M.475, V.478, M.482, S.488, G.489, V.492 Ligands: POV.6, POV.15 Ligand excluded by PLIP POV.5: 18 residues within 4Å: Chain A: W.535, A.538, V.539, L.542, Y.549, Q.553, D.565, Y.566, P.567, L.570 Chain D: I.381, T.384, M.385, I.388, Y.389 Ligands: PCW.3, POV.38, POV.39 Ligand excluded by PLIP POV.6: 13 residues within 4Å: Chain A: P.464, L.468, T.471, Q.523, K.524, I.526, F.527, G.528, R.624 Chain B: I.604 Ligands: Y01.2, POV.4, POV.15 Ligand excluded by PLIP POV.7: 14 residues within 4Å: Chain A: F.383, C.386, C.387, L.413, L.426, E.429, T.432, V.433, V.476, T.479, M.480, R.483, L.484, M.494 Ligand excluded by PLIP POV.8: 3 residues within 4Å: Chain A: F.474, V.478, M.482 Ligand excluded by PLIP POV.9: 19 residues within 4Å: Chain A: R.366, C.370, G.373, A.374, L.377, L.378, V.505, M.506, F.508, G.511, F.512, Q.513, M.514, L.515 Chain B: W.535, L.536, V.539 Ligands: PCW.18, POV.20 Ligand excluded by PLIP POV.10: 11 residues within 4Å: Chain A: L.378, C.382, M.385, Y.389, K.421, I.424, R.425, G.428 Ligands: Y01.1, PCW.18, POV.20 Ligand excluded by PLIP POV.12: 9 residues within 4Å: Chain A: P.592, F.593, I.597 Chain D: F.496, M.531 Ligands: Y01.11, Y01.43, POV.45, POV.47 Ligand excluded by PLIP POV.15: 8 residues within 4Å: Chain A: F.496, M.531 Chain B: P.592, F.593, I.597 Ligands: POV.4, POV.6, Y01.14 Ligand excluded by PLIP POV.19: 7 residues within 4Å: Chain B: M.475, V.478, M.482, S.488, V.492 Ligands: POV.21, POV.27 Ligand excluded by PLIP POV.20: 18 residues within 4Å: Chain A: I.381, T.384, M.385, I.388, Y.389 Chain B: W.535, A.538, V.539, L.542, Y.549, Q.553, D.565, Y.566, P.567, L.570 Ligands: POV.9, POV.10, PCW.18 Ligand excluded by PLIP POV.21: 14 residues within 4Å: Chain B: P.464, L.468, T.471, F.496, Q.523, K.524, I.526, F.527, G.528, R.624 Chain C: I.604 Ligands: Y01.17, POV.19, POV.27 Ligand excluded by PLIP POV.22: 14 residues within 4Å: Chain B: F.383, C.386, C.387, L.413, Y.417, L.426, E.429, T.432, V.476, T.479, M.480, R.483, L.484, M.494 Ligand excluded by PLIP POV.23: 3 residues within 4Å: Chain B: F.474, V.478, M.482 Ligand excluded by PLIP POV.24: 19 residues within 4Å: Chain B: R.366, C.370, G.373, A.374, L.377, L.378, V.505, M.506, F.508, G.511, F.512, Q.513, M.514, L.515 Chain C: W.535, L.536, V.539 Ligands: PCW.30, POV.32 Ligand excluded by PLIP POV.25: 11 residues within 4Å: Chain B: L.378, C.382, M.385, Y.389, K.421, I.424, R.425, G.428 Ligands: Y01.16, PCW.30, POV.32 Ligand excluded by PLIP POV.27: 9 residues within 4Å: Chain B: F.496, M.531 Chain C: P.592, F.593, I.597 Ligands: Y01.17, POV.19, POV.21, Y01.26 Ligand excluded by PLIP POV.31: 7 residues within 4Å: Chain C: M.475, M.482, S.488, G.489, V.492 Ligands: POV.33, POV.41 Ligand excluded by PLIP POV.32: 18 residues within 4Å: Chain B: I.381, T.384, M.385, I.388, Y.389 Chain C: W.535, A.538, V.539, L.542, Y.549, Q.553, D.565, Y.566, P.567, L.570 Ligands: POV.24, POV.25, PCW.30 Ligand excluded by PLIP POV.33: 15 residues within 4Å: Chain C: P.464, L.468, T.471, F.496, Q.523, K.524, I.526, F.527, G.528, R.624 Chain D: A.601, I.604 Ligands: Y01.29, POV.31, POV.41 Ligand excluded by PLIP POV.34: 14 residues within 4Å: Chain C: F.383, C.386, C.387, L.413, Y.417, L.426, E.429, T.432, V.476, T.479, M.480, R.483, L.484, M.494 Ligand excluded by PLIP POV.35: 4 residues within 4Å: Chain C: F.474, V.478, V.481, M.482 Ligand excluded by PLIP POV.36: 19 residues within 4Å: Chain C: R.366, C.370, G.373, A.374, L.377, L.378, V.505, M.506, F.508, G.511, F.512, Q.513, M.514, L.515 Chain D: W.535, L.536, V.539 Ligands: PCW.44, POV.46 Ligand excluded by PLIP POV.37: 11 residues within 4Å: Chain C: L.378, C.382, M.385, Y.389, K.421, I.424, R.425, G.428 Ligands: Y01.28, PCW.44, POV.46 Ligand excluded by PLIP POV.38: 19 residues within 4Å: Chain A: W.535, L.536, V.539 Chain D: R.366, C.370, G.373, A.374, L.377, L.378, V.505, M.506, F.508, G.511, F.512, Q.513, M.514, L.515 Ligands: PCW.3, POV.5 Ligand excluded by PLIP POV.39: 11 residues within 4Å: Chain D: L.378, C.382, M.385, Y.389, K.421, I.424, R.425, G.428 Ligands: PCW.3, POV.5, Y01.42 Ligand excluded by PLIP POV.41: 9 residues within 4Å: Chain C: F.496, M.531 Chain D: P.592, F.593, I.597 Ligands: Y01.29, POV.31, POV.33, Y01.40 Ligand excluded by PLIP POV.45: 7 residues within 4Å: Chain D: M.475, V.478, M.482, S.488, V.492 Ligands: POV.12, POV.47 Ligand excluded by PLIP POV.46: 16 residues within 4Å: Chain C: I.381, T.384, M.385, I.388, Y.389 Chain D: W.535, L.542, Y.549, Q.553, D.565, Y.566, P.567, L.570 Ligands: POV.36, POV.37, PCW.44 Ligand excluded by PLIP POV.47: 14 residues within 4Å: Chain A: I.604 Chain D: P.464, L.468, T.471, F.496, Q.523, K.524, I.526, F.527, G.528, R.624 Ligands: POV.12, Y01.43, POV.45 Ligand excluded by PLIP POV.48: 15 residues within 4Å: Chain D: F.383, C.386, C.387, L.413, Y.417, L.426, E.429, T.432, V.433, V.476, T.479, M.480, R.483, L.484, M.494 Ligand excluded by PLIP POV.49: 4 residues within 4Å: Chain D: F.474, V.478, V.481, M.482 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 4 residues within 4Å: Chain A: D.582 Chain B: D.582 Chain C: D.582 Chain D: D.582 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Metal complexes: C:D.582, A:D.582, A:D.582, D:D.582, B:D.582

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuberger, A. et al., Structure-function analyses of human oncochannel TRPV6 variants associated with a racial divergence in susceptibility to cancer. Structure (2024)

Release Date

2024-11-13

Peptides

Transient receptor potential cation channel subfamily V member 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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Transient receptor potential cation channel subfamily V member 6

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