SMTL ID : 9cui.1

Structure of human full-length ancestral 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: 16 residues within 4Å: Chain A: L.372, Y.376, Y.379, V.431, I.434, G.435, I.438, V.442, E.443, G.463, F.465, H.466, Y.507, F.508, M.643 Ligands: PCW.12 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.372, A:Y.376, A:Y.379, A:Y.379, A:I.434, A:I.438, A:V.442, A:Y.507 Salt bridges: A:H.466, A:H.466, A:R.510 Y01.14: 12 residues within 4Å: Chain A: P.592, F.593, S.596, I.604 Chain D: L.530, M.531, C.534, M.537, P.567, M.568, F.571 Ligands: PCW.52 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.530, D:F.571, D:F.571 Hydrogen bonds: A:P.592 Y01.18: 13 residues within 4Å: Chain A: C.534, I.541, P.567, F.571, F.574 Chain B: D.590, L.591, F.593, S.596, I.597, I.604 Ligands: PCW.3, PCW.19 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.593, B:F.593, B:I.597, B:I.604, A:I.541, A:P.567, A:F.571, A:F.574 Hydrogen bonds: B:L.591 Y01.20: 13 residues within 4Å: Chain B: L.372, Y.376, Y.379, V.431, G.435, V.442, E.443, F.465, H.466, Y.507, F.508, M.643 Ligands: PCW.30 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.372, B:Y.376, B:Y.379, B:Y.379, B:V.442, B:F.465, B:Y.507, B:Y.507, B:F.508 Salt bridges: B:H.466, B:H.466 Y01.22: 10 residues within 4Å: Chain B: C.534, A.538, I.541, P.567 Chain C: L.591, F.593, S.596, I.597, A.600 Ligands: PCW.23 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.593, C:F.593, C:I.597, C:A.600, B:I.541, B:P.567 Hydrogen bonds: C:S.596 Y01.34: 15 residues within 4Å: Chain C: I.375, Y.376, Y.379, V.431, G.435, I.438, V.442, E.443, G.463, F.465, H.466, Y.507, F.508, M.643 Ligands: PCW.44 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.375, C:Y.376, C:Y.379, C:Y.379, C:I.438, C:V.442, C:F.465, C:Y.507, C:Y.507 Salt bridges: C:H.466, C:H.466 Y01.36: 11 residues within 4Å: Chain C: C.534, A.538, I.541, P.567, M.568, F.571 Chain D: F.593, S.596, I.604 Ligands: PCW.37, PCW.48 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.604, C:A.538, C:I.541, C:F.571 Hydrogen bonds: D:S.596 Y01.50: 14 residues within 4Å: Chain D: L.372, Y.376, Y.379, V.431, G.435, I.438, V.442, E.443, F.465, H.466, I.469, Y.507, F.508 Ligands: PCW.47 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.372, D:Y.376, D:Y.379, D:V.431, D:I.438, D:V.442, D:E.443, D:H.466, D:I.469, D:Y.507, D:F.508 Hydrogen bonds: D:Y.507

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 13 residues within 4Å: Chain A: P.464, F.465, S.495, F.496, V.499, C.503, M.506, T.519, Q.523, I.526 Chain B: T.598, A.601 Ligands: PCW.4 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.464, A:F.496, A:F.496, A:Q.523, A:I.526, B:A.601 Hydrogen bonds: A:Q.523 CLR.21: 13 residues within 4Å: Chain B: P.464, F.465, F.496, V.499, M.506, T.519, I.522, Q.523, I.526, F.527 Chain C: T.598, A.601 Ligands: PCW.24 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.464, B:P.464, B:F.496, B:V.499, B:I.522, B:I.526, B:F.527, C:A.601 Hydrogen bonds: B:Q.523 CLR.35: 15 residues within 4Å: Chain C: F.465, F.496, V.499, C.503, M.506, T.519, I.522, Q.523, I.526 Chain D: M.594, I.597, T.598, A.601, I.605 Ligands: PCW.38 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.496, C:V.499, C:V.499, C:I.522, C:Q.523, C:I.526, D:I.597, D:A.601 Hydrogen bonds: C:Q.523 CLR.51: 13 residues within 4Å: Chain A: T.598, A.601 Chain D: P.464, F.465, F.496, V.499, C.503, M.506, T.519, I.522, Q.523, I.526 Ligands: PCW.53 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:P.464, D:F.496, D:V.499, D:Q.523, D:I.526 Hydrogen bonds: D:Q.523

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

PCW.3: 14 residues within 4Å: Chain A: C.534, W.535, A.538, L.542, Y.549, Y.566, P.567 Chain D: I.381, M.385, I.388, Y.389 Ligands: PCW.8, Y01.18, PCW.19 Ligand excluded by PLIP PCW.4: 9 residues within 4Å: Chain A: I.460, L.461, P.464, V.467, L.468, F.496, L.500, F.527 Ligands: CLR.2 Ligand excluded by PLIP PCW.5: 4 residues within 4Å: Chain A: F.496 Chain B: F.593 Ligands: PCW.6, PCW.19 Ligand excluded by PLIP PCW.6: 3 residues within 4Å: Chain A: M.482, G.489 Ligands: PCW.5 Ligand excluded by PLIP PCW.7: 1 residues within 4Å: Chain A: M.482 Ligand excluded by PLIP PCW.8: 1 residues within 4Å: Ligands: PCW.3 Ligand excluded by PLIP PCW.9: 6 residues within 4Å: Chain A: C.386, Y.417, E.429, L.430, T.479, M.494 Ligand excluded by PLIP PCW.10: 3 residues within 4Å: Chain A: F.512 Chain B: W.535 Ligands: PCW.11 Ligand excluded by PLIP PCW.11: 10 residues within 4Å: Chain A: R.366, P.367, C.370, M.371, A.374, L.377, F.508, F.512 Chain B: V.539 Ligands: PCW.10 Ligand excluded by PLIP PCW.12: 11 residues within 4Å: Chain A: L.378, C.382, M.385, Y.389, K.421, I.424, R.425, V.427 Ligands: Y01.1, PCW.13, PCW.23 Ligand excluded by PLIP PCW.13: 2 residues within 4Å: Ligands: PCW.12, PCW.23 Ligand excluded by PLIP PCW.15: 3 residues within 4Å: Chain A: F.593 Ligands: PCW.52, PCW.54 Ligand excluded by PLIP PCW.19: 4 residues within 4Å: Chain B: F.593 Ligands: PCW.3, PCW.5, Y01.18 Ligand excluded by PLIP PCW.23: 13 residues within 4Å: Chain A: I.381, M.385, Y.389 Chain B: V.539, L.542, Y.549, D.565, Y.566, P.567 Ligands: PCW.12, PCW.13, Y01.22, PCW.32 Ligand excluded by PLIP PCW.24: 6 residues within 4Å: Chain B: I.460, L.461, V.467, L.468, F.527 Ligands: CLR.21 Ligand excluded by PLIP PCW.25: 4 residues within 4Å: Chain B: M.475, M.482, S.488 Ligands: PCW.33 Ligand excluded by PLIP PCW.26: 1 residues within 4Å: Chain B: M.482 Ligand excluded by PLIP PCW.27: 9 residues within 4Å: Chain B: F.383, C.386, E.415, E.429, V.433, T.479, M.480, R.483, L.484 Ligand excluded by PLIP PCW.28: 10 residues within 4Å: Chain B: G.373, L.377, V.505, F.508, A.509, L.515 Chain C: L.536, V.539 Ligands: PCW.29, PCW.37 Ligand excluded by PLIP PCW.29: 9 residues within 4Å: Chain B: R.366, C.370, A.374, F.512, M.514, L.515 Chain C: F.63, W.535 Ligands: PCW.28 Ligand excluded by PLIP PCW.30: 12 residues within 4Å: Chain B: I.375, L.377, L.378, I.381, C.382, M.385, Y.389, K.421, I.424, G.428 Ligands: Y01.20, PCW.37 Ligand excluded by PLIP PCW.32: 3 residues within 4Å: Chain C: F.593 Ligands: PCW.23, PCW.33 Ligand excluded by PLIP PCW.33: 5 residues within 4Å: Chain B: F.496 Chain C: F.593, I.597 Ligands: PCW.25, PCW.32 Ligand excluded by PLIP PCW.37: 16 residues within 4Å: Chain B: L.377, I.381, M.385, Y.389 Chain C: C.534, W.535, A.538, L.542, Y.549, D.565, Y.566, P.567 Ligands: PCW.28, PCW.30, Y01.36, PCW.48 Ligand excluded by PLIP PCW.38: 7 residues within 4Å: Chain C: I.460, L.461, V.467, L.468, F.496, F.527 Ligands: CLR.35 Ligand excluded by PLIP PCW.39: 3 residues within 4Å: Chain C: M.482, G.489 Ligands: PCW.49 Ligand excluded by PLIP PCW.40: 2 residues within 4Å: Chain C: F.474, M.482 Ligand excluded by PLIP PCW.41: 6 residues within 4Å: Chain C: F.383, Y.417, E.429, V.433, T.479, M.494 Ligand excluded by PLIP PCW.42: 6 residues within 4Å: Chain C: F.512, Q.513, M.514, L.515 Chain D: W.535 Ligands: PCW.43 Ligand excluded by PLIP PCW.43: 15 residues within 4Å: Chain C: R.366, C.370, M.371, G.373, I.375, V.505, F.508, A.509, F.512, L.515 Chain D: F.63, R.65, W.535, V.539 Ligands: PCW.42 Ligand excluded by PLIP PCW.44: 9 residues within 4Å: Chain C: L.378, I.381, C.382, M.385, C.386, Y.389, K.421 Ligands: Y01.34, PCW.52 Ligand excluded by PLIP PCW.45: 5 residues within 4Å: Chain A: W.535 Chain D: F.512, Q.513, M.514 Ligands: PCW.46 Ligand excluded by PLIP PCW.46: 10 residues within 4Å: Chain A: V.539 Chain D: R.366, C.370, M.371, A.374, V.505, F.508, F.512, L.515 Ligands: PCW.45 Ligand excluded by PLIP PCW.47: 9 residues within 4Å: Chain D: L.377, L.378, C.382, M.385, Y.389, K.421, I.424, R.425 Ligands: Y01.50 Ligand excluded by PLIP PCW.48: 4 residues within 4Å: Chain D: F.593 Ligands: Y01.36, PCW.37, PCW.49 Ligand excluded by PLIP PCW.49: 4 residues within 4Å: Chain C: F.496 Chain D: F.593 Ligands: PCW.39, PCW.48 Ligand excluded by PLIP PCW.52: 15 residues within 4Å: Chain C: L.377, M.385, I.388, Y.389, W.502 Chain D: C.534, W.535, A.538, Y.549, Q.553, Y.566, P.567 Ligands: Y01.14, PCW.15, PCW.44 Ligand excluded by PLIP PCW.53: 8 residues within 4Å: Chain D: I.460, L.461, G.462, P.464, V.467, L.468, F.527 Ligands: CLR.51 Ligand excluded by PLIP PCW.54: 5 residues within 4Å: Chain A: F.593 Chain D: V.492, F.496 Ligands: PCW.15, PCW.55 Ligand excluded by PLIP PCW.55: 3 residues within 4Å: Chain D: M.475, M.482 Ligands: PCW.54 Ligand excluded by PLIP PCW.56: 1 residues within 4Å: Chain D: M.482 Ligand excluded by PLIP PCW.57: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.58: 10 residues within 4Å: Chain D: F.383, C.386, Y.417, L.426, E.429, T.432, V.433, T.479, M.480, R.483 Ligand excluded by PLIP

7 x CA: CALCIUM ION(Non-covalent)

CA.16: 5 residues within 4Å: Chain A: D.582 Chain B: D.582 Chain C: D.582 Chain D: D.582 Ligands: CA.17 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Metal complexes: B:D.582, C:D.582, D:D.582, A:D.582 CA.17: 4 residues within 4Å: Chain A: D.582 Chain B: D.582 Ligands: CA.16, CA.31 No protein-ligand interaction detected (PLIP) CA.31: 3 residues within 4Å: Chain B: T.579 Chain C: T.579 Ligands: CA.17 No protein-ligand interaction detected (PLIP) CA.59: 5 residues within 4Å: Chain E: D.21, D.23, T.27, T.29, E.32 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.23, E:T.27, E:E.32 CA.60: 5 residues within 4Å: Chain E: D.59, N.61, T.63, D.65, E.68 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.59, E:T.63, 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 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.132, E:D.134, E:Q.136, E:E.141, E:E.141

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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