SMTL ID : 8foa.1

Cryo-EM structure of human TRPV6 in complex with the natural phytoestrogen genistein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 18 residues within 4Å: Chain A: L.332, I.335, Y.336, G.395, I.398, I.399, V.402, T.419, I.420, L.421, G.422, H.426, F.468, T.600, M.603, L.604, K.607 Ligands: POV.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.335, A:Y.336, A:I.398, A:I.399, A:V.402, A:F.468, A:M.603, A:L.604 Hydrogen bonds: A:T.419, A:L.421 Salt bridges: A:H.426, A:K.607 Y01.2: 15 residues within 4Å: Chain A: L.428, C.463, M.466, Y.467, R.470, Q.483, F.487 Chain B: I.557, A.561, I.565, L.568, N.572 Ligands: Y01.3, POV.6, POV.17 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.483, B:I.565, B:I.565, B:L.568 Salt bridges: A:R.470 Hydrogen bonds: B:N.572, B:N.572 Y01.3: 18 residues within 4Å: Chain A: C.494, M.497, I.501, Y.524, D.525, P.527, M.528, L.530, F.531, F.534, F.537 Chain B: F.553, S.556, I.557, A.560 Ligands: Y01.2, POV.5, POV.6 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:M.497, A:I.501, A:P.527, A:L.530, A:F.531, A:F.531, A:F.534, A:F.537, B:I.557, B:A.560 Hydrogen bonds: B:S.556 Y01.12: 15 residues within 4Å: Chain A: F.553, S.556, I.557, A.560, I.564 Chain D: C.494, M.497, P.527, M.528, L.530, F.531, F.534 Ligands: POV.13, POV.48, POV.49 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:L.530, D:F.531, D:F.534, A:F.553, A:I.557, A:A.560, A:I.564 Y01.18: 17 residues within 4Å: Chain B: L.332, Y.336, Y.339, I.394, G.395, I.398, I.399, V.402, G.422, G.423, F.425, H.426, I.429, Y.467, R.470, M.603 Ligands: POV.29 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.332, B:Y.339, B:Y.339, B:I.394, B:I.398, B:I.399, B:V.402, B:I.429, B:Y.467 Hydrogen bonds: B:Y.467 Salt bridges: B:H.426, B:H.426, B:R.470 Y01.19: 11 residues within 4Å: Chain B: P.424, S.455, F.456, L.460, Q.483, M.485 Chain C: I.557, T.558, A.561, I.565 Ligands: POV.23 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.561, C:I.565, B:P.424, B:F.456, B:L.460 Y01.20: 14 residues within 4Å: Chain B: C.494, P.527, M.528, L.530, F.531, F.534 Chain C: F.553, S.556, I.557, A.560, I.564 Ligands: POV.22, POV.23, POV.30 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.557, C:A.560, C:I.564, B:P.527, B:L.530, B:F.531, B:F.534 Y01.31: 17 residues within 4Å: Chain C: L.332, I.335, Y.336, G.395, I.399, V.402, E.403, F.416, T.419, L.421, F.425, H.426, I.429, F.468, T.600, M.603, L.604 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.332, C:Y.336, C:I.399, C:V.402, C:L.421, C:F.425, C:I.429, C:F.468, C:M.603, C:L.604 Hydrogen bonds: C:L.421 Salt bridges: C:H.426, C:K.607 Y01.32: 16 residues within 4Å: Chain C: S.455, F.456, V.459, L.460, C.463, M.466, Y.467, R.470, Q.483, K.484, F.487 Chain D: I.557, T.558, I.565, L.568 Ligands: POV.35 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.456, C:V.459, C:V.459, C:L.460, C:Q.483, C:F.487, D:I.557, D:I.565, D:I.565, D:L.568 Hydrogen bonds: C:Q.483 Salt bridges: C:K.484 Y01.33: 17 residues within 4Å: Chain C: C.494, M.497, I.501, Y.524, D.525, P.527, M.528, L.530, F.531, F.534, F.537 Chain D: F.553, S.556, I.557, A.560 Ligands: POV.28, POV.35 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:M.497, C:L.530, C:F.531, C:F.531, C:F.537, D:F.553, D:I.557, D:A.560 Hydrogen bonds: D:S.556 Y01.44: 17 residues within 4Å: Chain D: L.332, Y.336, Y.339, G.395, I.398, I.399, E.403, G.422, G.423, P.424, F.425, H.426, I.429, Y.467, M.603 Ligands: POV.42, POV.50 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.332, D:Y.336, D:Y.339, D:Y.339, D:I.398, D:I.399, D:F.425, D:I.429, D:Y.467 Salt bridges: D:H.426, D:H.426, D:R.470 Y01.45: 14 residues within 4Å: Chain A: M.554, I.557, T.558, A.561, I.565 Chain D: P.424, S.455, F.456, V.459, L.460, Q.483, M.485, F.487 Ligands: POV.49 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.456, D:F.456, D:V.459, D:F.487, A:T.558, A:A.561, A:I.565

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

POV.4: 4 residues within 4Å: Chain A: M.435, S.448, G.449 Ligands: POV.17 Ligand excluded by PLIP POV.5: 18 residues within 4Å: Chain A: C.494, W.495, A.498, V.499, L.502, Y.509, Q.513, D.525, Y.526, P.527 Chain D: I.341, M.345, I.348, Y.349 Ligands: Y01.3, POV.6, POV.41, POV.42 Ligand excluded by PLIP POV.6: 17 residues within 4Å: Chain A: F.416, G.423, P.424, L.428, K.484, M.485, G.488, M.491, R.492, C.494, W.495, R.584, L.592 Chain D: M.474 Ligands: Y01.2, Y01.3, POV.5 Ligand excluded by PLIP POV.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP POV.8: 10 residues within 4Å: Chain A: F.343, C.347, L.373, L.386, E.389, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.9: 2 residues within 4Å: Chain A: I.445, A.447 Ligand excluded by PLIP POV.10: 12 residues within 4Å: Chain A: R.326, A.334, L.337, F.472, Q.473, M.474, T.479 Chain B: G.488, R.492, W.495, D.580 Ligands: POV.11 Ligand excluded by PLIP POV.11: 11 residues within 4Å: Chain A: L.338, I.341, M.345, C.346, Y.349, K.381, D.382, R.385 Ligands: Y01.1, POV.10, POV.22 Ligand excluded by PLIP POV.13: 6 residues within 4Å: Chain A: F.553 Chain D: V.452 Ligands: Y01.12, POV.47, POV.48, POV.49 Ligand excluded by PLIP POV.17: 5 residues within 4Å: Chain A: V.452, F.456 Chain B: F.553 Ligands: Y01.2, POV.4 Ligand excluded by PLIP POV.21: 3 residues within 4Å: Chain B: S.448, G.449 Ligands: POV.30 Ligand excluded by PLIP POV.22: 13 residues within 4Å: Chain A: I.341, M.345, I.348, Y.349 Chain B: W.495, L.502, Y.509, Y.524, D.525, Y.526, P.527 Ligands: POV.11, Y01.20 Ligand excluded by PLIP POV.23: 9 residues within 4Å: Chain B: I.420, T.431, F.487, L.490, M.491 Chain C: I.557, I.564 Ligands: Y01.19, Y01.20 Ligand excluded by PLIP POV.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP POV.25: 12 residues within 4Å: Chain B: F.343, C.346, C.347, Y.377, E.389, L.390, V.393, V.436, T.439, M.440, L.444, M.454 Ligand excluded by PLIP POV.26: 1 residues within 4Å: Chain B: I.445 Ligand excluded by PLIP POV.27: 15 residues within 4Å: Chain B: R.326, P.327, C.330, M.331, G.333, A.334, V.465, M.466, F.468, A.469, F.472 Chain C: W.495, V.499 Ligands: POV.28, POV.29 Ligand excluded by PLIP POV.28: 16 residues within 4Å: Chain B: L.337, I.341, I.348, Y.349 Chain C: C.494, W.495, V.499, L.502, Y.509, D.525, Y.526, P.527 Ligands: POV.27, POV.29, Y01.33, POV.35 Ligand excluded by PLIP POV.29: 13 residues within 4Å: Chain B: I.335, Y.339, I.341, M.345, C.346, Y.349, K.381, D.382, I.384, G.388 Ligands: Y01.18, POV.27, POV.28 Ligand excluded by PLIP POV.30: 8 residues within 4Å: Chain B: G.449, V.451, V.452 Chain C: F.553, M.554, I.557 Ligands: Y01.20, POV.21 Ligand excluded by PLIP POV.34: 2 residues within 4Å: Chain C: S.448, G.449 Ligand excluded by PLIP POV.35: 14 residues within 4Å: Chain B: M.474 Chain C: F.415, P.424, V.427, L.428, K.484, M.485, G.488, M.491, R.492, W.495 Ligands: POV.28, Y01.32, Y01.33 Ligand excluded by PLIP POV.36: 1 residues within 4Å: Chain C: V.402 Ligand excluded by PLIP POV.37: 10 residues within 4Å: Chain C: F.343, C.346, C.347, L.386, E.389, T.392, T.439, R.443, L.444, M.454 Ligand excluded by PLIP POV.38: 3 residues within 4Å: Chain C: F.434, V.438, I.445 Ligand excluded by PLIP POV.39: 11 residues within 4Å: Chain C: L.337, L.338, I.341, C.342, M.345, Y.349, K.381, D.382, I.384, R.385 Ligands: POV.48 Ligand excluded by PLIP POV.41: 12 residues within 4Å: Chain A: W.495 Chain D: R.326, C.330, G.333, A.334, L.337, L.338, V.465, F.468, F.472 Ligands: POV.5, POV.42 Ligand excluded by PLIP POV.42: 14 residues within 4Å: Chain D: L.338, M.345, C.346, Y.349, K.371, T.379, K.381, D.382, I.384, R.385, G.388 Ligands: POV.5, POV.41, Y01.44 Ligand excluded by PLIP POV.43: 2 residues within 4Å: Chain C: V.452 Chain D: F.553 Ligand excluded by PLIP POV.46: 14 residues within 4Å: Chain C: R.326, L.337, A.469, F.472, Q.473, M.474, G.476, P.477, T.479 Chain D: F.487, G.488, D.489, M.491, R.492 Ligand excluded by PLIP POV.47: 6 residues within 4Å: Chain D: M.435, M.442, S.448, G.449 Ligands: POV.13, POV.49 Ligand excluded by PLIP POV.48: 14 residues within 4Å: Chain C: I.341, M.345, I.348, Y.349 Chain D: C.494, W.495, L.502, Y.509, D.525, Y.526, P.527 Ligands: Y01.12, POV.13, POV.39 Ligand excluded by PLIP POV.49: 12 residues within 4Å: Chain A: I.557, A.561, I.564 Chain D: I.420, F.456, F.487, L.490, M.491 Ligands: Y01.12, POV.13, Y01.45, POV.47 Ligand excluded by PLIP POV.50: 2 residues within 4Å: Chain D: V.402 Ligands: Y01.44 Ligand excluded by PLIP POV.51: 13 residues within 4Å: Chain D: F.343, C.346, C.347, L.373, Y.377, L.386, E.389, T.392, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 4 residues within 4Å: Chain A: H.582, H.587 Chain D: W.583, H.587 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Metal complexes: A:H.582, A:H.587, D:H.587 ZN.40: 4 residues within 4Å: Chain B: W.583, H.587 Chain C: H.582, H.587 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Metal complexes: B:H.587, C:H.582, C:H.587

1 x CA: CALCIUM ION(Non-covalent)

CA.15: 4 residues within 4Å: Chain A: D.542 Chain B: D.542 Chain C: D.542 Chain D: D.542 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 2 interactions with chain D Metal complexes: C:D.542, B:D.542, A:D.542, D:D.542, D:D.542

2 x GEN: GENISTEIN(Non-covalent)

GEN.16: 11 residues within 4Å: Chain A: M.570, L.571, L.573, L.574 Chain B: L.571, L.574 Chain C: M.570, L.571, L.574 Chain D: L.571, L.574 8 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:L.574, C:L.571, C:L.574, C:L.574, B:L.571, D:L.574 Hydrogen bonds: A:M.570, C:M.570 GEN.53: 8 residues within 4Å: Chain A: M.578, G.579 Chain B: W.583 Chain C: M.578 Chain D: M.578, H.582, W.583, A.586 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:M.578, D:W.583, D:W.583

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuberger, A. et al., Structural mechanism of human oncochannel TRPV6 inhibition by the natural phytoestrogen genistein. Nat Commun (2023)

Release Date

2023-05-24

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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