SMTL ID : 9cuk.1

Structure of human full-length derived TRPV6 channel in Calmodulin-bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 18 residues within 4Å: Chain A: L.372, I.375, Y.376, Y.379, V.431, I.434, G.435, I.438, I.439, V.442, T.459, G.462, G.463, F.465, H.466, I.469, Y.507 Ligands: PCW.11 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.372, A:I.375, A:Y.376, A:Y.379, A:Y.379, A:I.434, A:I.438, A:I.439, A:V.442, A:F.465, A:Y.507, A:Y.507 Hydrogen bonds: A:F.465, A:H.466 Salt bridges: A:H.466, A:H.466 Y01.12: 11 residues within 4Å: Chain A: S.596, I.604 Chain D: C.534, M.537, A.538, I.541, P.567, M.568, F.571 Ligands: PCW.13, PCW.53 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:S.596 Hydrophobic interactions: D:A.538, D:I.541, D:P.567, D:F.571, D:F.571 Y01.16: 13 residues within 4Å: Chain A: C.534, I.541, P.567, L.570, F.571, F.574 Chain B: D.590, L.591, P.592, F.593, S.596, I.597 Ligands: PCW.3 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.567, A:F.571, A:F.574, B:D.590, B:I.597 Hydrogen bonds: B:L.591, B:S.596 Y01.19: 16 residues within 4Å: Chain B: Y.376, Y.379, V.431, G.435, I.438, I.439, V.442, T.459, G.462, G.463, F.465, H.466, Y.507, F.508, M.643 Ligands: PCW.29 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.379, B:Y.379, B:V.431, B:I.438, B:I.439, B:V.442, B:F.465, B:Y.507, B:Y.507, B:F.508 Hydrogen bonds: B:G.463, B:F.465, B:H.466 Salt bridges: B:H.466, B:H.466 Y01.32: 12 residues within 4Å: Chain B: C.534, M.537, A.538, I.541, P.567, L.570 Chain C: L.591, P.592, S.596, I.597 Ligands: PCW.21, PCW.33 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:A.538, B:I.541, B:L.570, C:I.597 Hydrogen bonds: C:L.591, C:S.596 Y01.35: 17 residues within 4Å: Chain C: Y.376, Y.379, V.431, G.435, I.438, I.439, V.442, E.443, T.459, G.462, G.463, P.464, F.465, H.466, Y.507, F.508 Ligands: PCW.45 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.379, C:Y.379, C:V.431, C:I.438, C:I.439, C:V.442, C:Y.507, C:Y.507, C:F.508 Hydrogen bonds: C:G.463, C:F.465, C:H.466 Salt bridges: C:H.466, C:H.466 Y01.37: 16 residues within 4Å: Chain C: C.534, M.537, A.538, I.541, Y.564, D.565, P.567, M.568, L.570, F.571 Chain D: S.596, I.597, A.600, I.604 Ligands: PCW.38, PCW.49 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:A.538, C:I.541, C:P.567, C:L.570, C:F.571, D:I.597, D:A.600, D:I.604 Hydrogen bonds: C:Y.564, C:D.565 Y01.51: 12 residues within 4Å: Chain D: Y.376, Y.379, V.431, G.435, I.438, V.442, G.462, G.463, F.465, H.466, Y.507 Ligands: PCW.48 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.376, D:Y.379, D:V.431, D:I.438, D:V.442, D:F.465, D:Y.507, D:Y.507 Hydrogen bonds: D:G.463, D:H.466 Salt bridges: D:H.466, D:H.466

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 18 residues within 4Å: Chain A: P.464, F.465, L.468, S.495, F.496, V.499, C.503, M.506, T.519, I.522, Q.523, I.526 Chain B: I.597, T.598, A.601, I.605 Ligands: PCW.4, PCW.18 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:I.597, B:I.605, A:P.464, A:P.464, A:F.465, A:L.468, A:F.496, A:F.496, A:I.526 Hydrogen bonds: A:Q.523, A:Q.523 CLR.20: 15 residues within 4Å: Chain B: P.464, F.465, L.468, F.496, V.499, C.503, M.506, T.519, I.522, Q.523, I.526 Chain C: T.598, A.601, I.605 Ligands: PCW.22 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:I.605, B:P.464, B:P.464, B:F.465, B:L.468, B:F.496, B:Q.523, B:I.526 Hydrogen bonds: B:Q.523, B:Q.523 CLR.36: 13 residues within 4Å: Chain C: P.464, F.465, L.468, F.496, V.499, M.506, T.519, I.522, Q.523, I.526 Chain D: I.605 Ligands: PCW.39, PCW.50 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.464, C:P.464, C:F.465, C:L.468, C:F.496, C:V.499, C:I.526, D:I.605 Hydrogen bonds: C:Q.523 CLR.52: 16 residues within 4Å: Chain A: T.598, A.601, I.605 Chain D: P.464, F.465, L.468, F.496, V.499, L.500, M.506, T.519, I.522, Q.523, I.526 Ligands: PCW.14, PCW.54 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:P.464, D:P.464, D:F.465, D:L.468, D:F.496, D:F.496, D:I.522, D:I.526, A:A.601, A:I.605 Hydrogen bonds: D:Q.523, D:Q.523

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

PCW.3: 16 residues within 4Å: Chain A: C.534, W.535, A.538, V.539, Y.549, D.565, Y.566, P.567 Chain D: I.381, M.385, I.388, Y.389, W.502 Ligands: Y01.16, PCW.17, PCW.48 Ligand excluded by PLIP PCW.4: 8 residues within 4Å: Chain A: P.464, V.467, L.468, T.471, F.496, L.500, F.527 Ligands: CLR.2 Ligand excluded by PLIP PCW.5: 6 residues within 4Å: Chain A: M.475, M.482, G.489, V.492 Chain B: F.593 Ligands: PCW.18 Ligand excluded by PLIP PCW.6: 1 residues within 4Å: Chain A: M.482 Ligand excluded by PLIP PCW.7: 1 residues within 4Å: Ligands: PCW.48 Ligand excluded by PLIP PCW.8: 7 residues within 4Å: Chain A: F.383, L.426, E.429, T.432, V.433, T.479, L.484 Ligand excluded by PLIP PCW.9: 3 residues within 4Å: Chain A: P.367, C.370, M.371 Ligand excluded by PLIP PCW.10: 12 residues within 4Å: Chain A: G.373, L.377, L.378, F.508, A.509, F.512, Q.513, M.514, L.515 Chain B: W.535 Ligands: PCW.11, PCW.21 Ligand excluded by PLIP PCW.11: 10 residues within 4Å: Chain A: I.381, M.385, Y.389, K.421, I.424, V.427 Ligands: Y01.1, PCW.10, PCW.21, PCW.25 Ligand excluded by PLIP PCW.13: 3 residues within 4Å: Ligands: Y01.12, PCW.14, PCW.53 Ligand excluded by PLIP PCW.14: 7 residues within 4Å: Chain A: F.593, I.597 Chain D: F.496 Ligands: PCW.13, CLR.52, PCW.54, PCW.55 Ligand excluded by PLIP PCW.17: 2 residues within 4Å: Ligands: PCW.3, PCW.18 Ligand excluded by PLIP PCW.18: 5 residues within 4Å: Chain A: F.496 Chain B: F.593 Ligands: CLR.2, PCW.5, PCW.17 Ligand excluded by PLIP PCW.21: 15 residues within 4Å: Chain A: I.381, M.385, I.388, Y.389 Chain B: C.534, W.535, A.538, L.542, Y.549, Y.566, P.567 Ligands: PCW.10, PCW.11, Y01.32, PCW.33 Ligand excluded by PLIP PCW.22: 4 residues within 4Å: Chain B: V.467, L.468, F.527 Ligands: CLR.20 Ligand excluded by PLIP PCW.23: 3 residues within 4Å: Chain B: M.475, M.482 Chain C: F.593 Ligand excluded by PLIP PCW.24: 1 residues within 4Å: Chain B: F.474 Ligand excluded by PLIP PCW.25: 1 residues within 4Å: Ligands: PCW.11 Ligand excluded by PLIP PCW.26: 10 residues within 4Å: Chain B: F.383, C.386, Y.417, E.429, L.430, T.432, V.433, T.479, M.480, L.484 Ligand excluded by PLIP PCW.27: 9 residues within 4Å: Chain B: C.370, G.373, V.505, F.508, A.509, L.515 Chain C: V.539 Ligands: PCW.28, PCW.38 Ligand excluded by PLIP PCW.28: 7 residues within 4Å: Chain B: R.366, M.371, F.512, M.514, L.515 Chain C: W.535 Ligands: PCW.27 Ligand excluded by PLIP PCW.29: 15 residues within 4Å: Chain B: I.375, L.377, L.378, I.381, C.382, M.385, C.386, Y.389, K.421, I.424, V.427, G.428, V.431 Ligands: Y01.19, PCW.38 Ligand excluded by PLIP PCW.33: 3 residues within 4Å: Ligands: PCW.21, Y01.32, PCW.34 Ligand excluded by PLIP PCW.34: 2 residues within 4Å: Chain C: I.597 Ligands: PCW.33 Ligand excluded by PLIP PCW.38: 18 residues within 4Å: Chain B: L.377, I.381, M.385, I.388, Y.389, W.502 Chain C: C.534, W.535, A.538, V.539, L.542, Y.549, D.565, Y.566, P.567 Ligands: PCW.27, PCW.29, Y01.37 Ligand excluded by PLIP PCW.39: 6 residues within 4Å: Chain C: P.464, F.496, L.500, Q.523, F.527 Ligands: CLR.36 Ligand excluded by PLIP PCW.40: 5 residues within 4Å: Chain C: M.475, M.482, G.489, V.492 Chain D: F.593 Ligand excluded by PLIP PCW.41: 1 residues within 4Å: Chain C: M.482 Ligand excluded by PLIP PCW.42: 8 residues within 4Å: Chain C: F.383, Y.417, E.429, T.432, V.433, V.476, T.479, M.480 Ligand excluded by PLIP PCW.43: 6 residues within 4Å: Chain C: F.512, Q.513, M.514, L.515 Chain D: W.535 Ligands: PCW.44 Ligand excluded by PLIP PCW.44: 12 residues within 4Å: Chain C: R.366, P.367, C.370, G.373, A.374, L.378, V.505, F.508, F.512, L.515 Ligands: PCW.43, PCW.45 Ligand excluded by PLIP PCW.45: 10 residues within 4Å: Chain C: L.377, L.378, C.382, M.385, Y.389, I.424, G.428 Ligands: Y01.35, PCW.44, PCW.53 Ligand excluded by PLIP PCW.46: 4 residues within 4Å: Chain A: W.535 Chain D: Q.513, M.514, L.515 Ligand excluded by PLIP PCW.47: 12 residues within 4Å: Chain A: L.536, V.539 Chain D: K.362, R.366, C.370, G.373, A.374, V.505, F.508, A.509, F.512, L.515 Ligand excluded by PLIP PCW.48: 11 residues within 4Å: Chain D: L.378, C.382, M.385, Y.389, K.421, I.424, G.428, V.431 Ligands: PCW.3, PCW.7, Y01.51 Ligand excluded by PLIP PCW.49: 2 residues within 4Å: Ligands: Y01.37, PCW.50 Ligand excluded by PLIP PCW.50: 4 residues within 4Å: Chain C: F.496 Chain D: I.597 Ligands: CLR.36, PCW.49 Ligand excluded by PLIP PCW.53: 15 residues within 4Å: Chain C: I.381, M.385, I.388, Y.389, W.502 Chain D: C.534, W.535, A.538, L.542, Y.549, Y.566, P.567 Ligands: Y01.12, PCW.13, PCW.45 Ligand excluded by PLIP PCW.54: 8 residues within 4Å: Chain D: P.464, V.467, L.468, M.475, F.527 Ligands: PCW.14, CLR.52, PCW.55 Ligand excluded by PLIP PCW.55: 5 residues within 4Å: Chain A: F.593 Chain D: M.475, M.482 Ligands: PCW.14, PCW.54 Ligand excluded by PLIP PCW.56: 1 residues within 4Å: Chain D: M.482 Ligand excluded by PLIP PCW.57: 1 residues within 4Å: Chain D: W.535 Ligand excluded by PLIP PCW.58: 8 residues within 4Å: Chain D: F.383, Y.417, E.429, T.479, M.480, R.483, L.484, M.494 Ligand excluded by PLIP

7 x CA: CALCIUM ION(Non-covalent)

CA.15: 5 residues within 4Å: Chain A: D.582 Chain B: D.582 Chain C: D.582 Chain D: D.582 Ligands: CA.30 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Metal complexes: A:D.582, B:D.582, C:D.582, D:D.582 CA.30: 4 residues within 4Å: Chain A: T.579, I.580 Chain B: T.579 Ligands: CA.15 No protein-ligand interaction detected (PLIP) CA.31: 2 residues within 4Å: Chain B: T.579 Chain C: T.579 No protein-ligand interaction detected (PLIP) CA.59: 5 residues within 4Å: Chain E: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.21, E:D.23, E:D.23, E:T.27, E:E.32 CA.60: 6 residues within 4Å: Chain E: D.57, D.59, N.61, T.63, D.65, E.68 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.59, E:D.59, E:T.63, E:E.68, E:E.68 CA.61: 6 residues within 4Å: Chain E: D.94, D.96, N.98, Y.100, S.102, E.105 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.94, E:D.96, E:Y.100, E:E.105, E:E.105 CA.62: 6 residues within 4Å: Chain E: D.130, D.132, D.134, Q.136, N.138, E.141 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.132, E:D.134, E:Q.136

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
Calmodulin-1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily V member 6

Calmodulin-1

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