SMTL ID : 8fob.1

Cryo-EM structure of human TRPV6 in the open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 16 residues within 4Å: Chain A: L.332, I.335, Y.336, Y.339, V.391, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, Y.467, M.603 Ligands: POV.9 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.332, A:L.332, A:I.335, A:Y.336, A:Y.339, A:Y.339, A:I.398, A:I.399, A:V.402, A:F.425, A:Y.467, A:Y.467 Hydrogen bonds: A:G.423, A:F.425 Salt bridges: A:H.426, A:H.426, A:R.470 Y01.2: 19 residues within 4Å: Chain A: P.424, F.425, F.456, V.459, C.463, R.470, T.479, I.480, I.482, Q.483, I.486, F.487, Q.596 Chain B: M.554, I.557, A.561, I.565 Ligands: POV.6, POV.15 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.424, A:F.456, A:V.459, A:I.480, A:I.482, A:I.486, A:F.487, B:I.557, B:A.561, B:I.565 Hydrogen bonds: A:T.479, A:T.479, A:Q.596 Salt bridges: A:R.470 Y01.10: 10 residues within 4Å: Chain A: F.553, S.556, A.560, I.564, L.568 Chain D: C.494, M.497, F.534, L.538 Ligands: POV.44 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:M.497, D:F.534, D:L.538, A:F.553, A:A.560, A:I.564, A:L.568 Hydrogen bonds: A:S.556, A:S.556 Y01.14: 13 residues within 4Å: Chain A: C.494, M.497, I.501, P.527, L.530, F.534, L.538 Chain B: F.553, S.556, A.560, I.564, L.568 Ligands: POV.5 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.553, B:A.560, B:I.564, B:L.568, A:M.497, A:I.501, A:F.534, A:L.538 Hydrogen bonds: B:S.556, B:S.556 Y01.16: 16 residues within 4Å: Chain B: L.332, I.335, Y.336, Y.339, V.391, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, Y.467, M.603 Ligands: POV.24 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.332, B:L.332, B:I.335, B:Y.336, B:Y.339, B:Y.339, B:I.398, B:I.399, B:V.402, B:F.425, B:Y.467, B:Y.467 Hydrogen bonds: B:G.423, B:F.425 Salt bridges: B:H.426, B:H.426, B:R.470 Y01.17: 17 residues within 4Å: Chain B: P.424, F.425, F.456, V.459, M.466, R.470, T.479, I.480, I.482, Q.483, I.486, Q.596 Chain C: I.557, A.561, I.565 Ligands: POV.21, POV.26 13 PLIP interactions: 3 interactions with chain C, 10 interactions with chain B Hydrophobic interactions: C:I.557, C:A.561, C:I.565, B:P.424, B:F.456, B:V.459, B:I.480, B:I.482, B:I.486 Hydrogen bonds: B:T.479, B:T.479, B:Q.596 Salt bridges: B:R.470 Y01.25: 13 residues within 4Å: Chain B: C.494, M.497, I.501, P.527, L.530, F.534, L.538 Chain C: F.553, S.556, A.560, I.564, L.568 Ligands: POV.20 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.553, C:A.560, C:I.564, C:L.568, B:M.497, B:I.501, B:F.534, B:L.538 Hydrogen bonds: C:S.556, C:S.556 Y01.27: 16 residues within 4Å: Chain C: L.332, I.335, Y.336, Y.339, V.391, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, Y.467, M.603 Ligands: POV.36 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.332, C:L.332, C:I.335, C:Y.336, C:Y.339, C:Y.339, C:I.398, C:I.399, C:V.402, C:F.425, C:Y.467, C:Y.467 Hydrogen bonds: C:G.423, C:F.425 Salt bridges: C:H.426, C:H.426, C:R.470 Y01.28: 19 residues within 4Å: Chain C: P.424, F.425, F.456, V.459, C.463, R.470, T.479, I.480, I.482, Q.483, I.486, F.487, Q.596 Chain D: M.554, I.557, A.561, I.565 Ligands: POV.33, POV.39 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:P.424, C:F.456, C:V.459, C:I.480, C:I.482, C:I.486, C:F.487, D:I.557, D:A.561, D:I.565 Hydrogen bonds: C:T.479, C:T.479, C:Q.596 Salt bridges: C:R.470 Y01.29: 13 residues within 4Å: Chain C: C.494, M.497, I.501, P.527, L.530, F.534, L.538 Chain D: F.553, S.556, A.560, I.564, L.568 Ligands: POV.32 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.553, D:A.560, D:I.564, D:I.564, D:L.568, C:M.497, C:I.501, C:F.534, C:L.538 Hydrogen bonds: D:S.556, D:S.556 Y01.40: 16 residues within 4Å: Chain D: L.332, I.335, Y.336, Y.339, V.391, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, Y.467, M.603 Ligands: POV.38 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.332, D:L.332, D:I.335, D:Y.336, D:Y.339, D:Y.339, D:V.391, D:I.398, D:I.399, D:V.402, D:F.425, D:Y.467, D:Y.467 Hydrogen bonds: D:G.423 Salt bridges: D:H.426, D:H.426, D:R.470 Y01.41: 18 residues within 4Å: Chain A: I.557, A.561, I.565 Chain D: P.424, F.425, F.456, V.459, C.463, R.470, T.479, I.480, I.482, Q.483, I.486, F.487, Q.596 Ligands: POV.11, POV.45 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain D Hydrophobic interactions: A:I.557, A:A.561, A:I.565, D:P.424, D:F.456, D:V.459, D:I.480, D:I.482, D:I.486, D:F.487 Hydrogen bonds: D:T.479, D:T.479, D:Q.596 Salt bridges: D:R.470

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

PCW.3: 6 residues within 4Å: Chain A: M.491, R.492, W.495 Chain D: F.472, L.475 Ligands: POV.5 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.472, D:F.472, D:F.472, D:L.475 PCW.18: 6 residues within 4Å: Chain A: F.472, L.475 Chain B: M.491, R.492, W.495 Ligands: POV.20 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.472, A:F.472, A:L.475 PCW.30: 6 residues within 4Å: Chain B: F.472, L.475 Chain C: M.491, R.492, W.495 Ligands: POV.32 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.472, B:F.472, B:L.475, B:L.475 PCW.42: 6 residues within 4Å: Chain C: F.472, L.475 Chain D: M.491, R.492, W.495 Ligands: POV.44 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.472, C:F.472, C:L.475, C:L.475

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

POV.4: 5 residues within 4Å: Chain A: M.435, G.449, V.452 Ligands: POV.6, POV.15 Ligand excluded by PLIP POV.5: 20 residues within 4Å: Chain A: C.494, W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527, L.530 Chain D: L.337, I.341, M.345, I.348, Y.349 Ligands: PCW.3, Y01.14, POV.15, POV.37, POV.38 Ligand excluded by PLIP POV.6: 3 residues within 4Å: Chain A: F.487 Ligands: Y01.2, POV.4 Ligand excluded by PLIP POV.7: 13 residues within 4Å: Chain A: F.343, C.346, C.347, Y.377, L.386, E.389, L.390, V.393, V.436, T.439, M.440, R.443, M.454 Ligand excluded by PLIP POV.8: 12 residues within 4Å: Chain A: P.327, C.330, G.333, V.465, M.466, F.468, A.469, L.475 Chain B: W.495, L.496, V.499 Ligands: POV.20 Ligand excluded by PLIP POV.9: 9 residues within 4Å: Chain A: L.338, I.341, C.342, M.345, C.346, Y.349, K.381 Ligands: Y01.1, POV.20 Ligand excluded by PLIP POV.11: 7 residues within 4Å: Chain A: F.553, I.557 Chain D: F.456, M.491 Ligands: Y01.41, POV.43, POV.44 Ligand excluded by PLIP POV.15: 8 residues within 4Å: Chain A: F.456, M.491 Chain B: F.553, I.557, I.564 Ligands: Y01.2, POV.4, POV.5 Ligand excluded by PLIP POV.19: 5 residues within 4Å: Chain B: M.435, G.449, V.452 Ligands: POV.21, POV.26 Ligand excluded by PLIP POV.20: 18 residues within 4Å: Chain A: M.345, I.348, Y.349 Chain B: C.494, W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527, L.530 Ligands: POV.8, POV.9, PCW.18, Y01.25, POV.26 Ligand excluded by PLIP POV.21: 4 residues within 4Å: Chain B: Q.483, F.487 Ligands: Y01.17, POV.19 Ligand excluded by PLIP POV.22: 12 residues within 4Å: Chain B: F.343, C.346, C.347, Y.377, L.386, E.389, L.390, V.436, T.439, M.440, R.443, M.454 Ligand excluded by PLIP POV.23: 11 residues within 4Å: Chain B: P.327, C.330, G.333, V.465, M.466, F.468, A.469 Chain C: W.495, L.496, V.499 Ligands: POV.32 Ligand excluded by PLIP POV.24: 9 residues within 4Å: Chain B: L.338, I.341, C.342, M.345, C.346, Y.349, K.381 Ligands: Y01.16, POV.32 Ligand excluded by PLIP POV.26: 8 residues within 4Å: Chain B: F.456, M.491 Chain C: F.553, I.557, I.564 Ligands: Y01.17, POV.19, POV.20 Ligand excluded by PLIP POV.31: 5 residues within 4Å: Chain C: M.435, G.449, V.452 Ligands: POV.33, POV.39 Ligand excluded by PLIP POV.32: 19 residues within 4Å: Chain B: I.341, M.345, I.348, Y.349 Chain C: C.494, W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527, L.530 Ligands: POV.23, POV.24, Y01.29, PCW.30, POV.39 Ligand excluded by PLIP POV.33: 3 residues within 4Å: Chain C: F.487 Ligands: Y01.28, POV.31 Ligand excluded by PLIP POV.34: 13 residues within 4Å: Chain C: F.343, C.346, C.347, Y.377, L.386, E.389, L.390, V.393, V.436, T.439, M.440, R.443, M.454 Ligand excluded by PLIP POV.35: 12 residues within 4Å: Chain C: P.327, C.330, G.333, V.465, M.466, F.468, A.469, L.475 Chain D: W.495, L.496, V.499 Ligands: POV.44 Ligand excluded by PLIP POV.36: 9 residues within 4Å: Chain C: L.338, I.341, C.342, M.345, C.346, Y.349, K.381 Ligands: Y01.27, POV.44 Ligand excluded by PLIP POV.37: 11 residues within 4Å: Chain A: W.495, L.496, V.499 Chain D: P.327, C.330, G.333, V.465, M.466, F.468, A.469 Ligands: POV.5 Ligand excluded by PLIP POV.38: 8 residues within 4Å: Chain D: I.341, C.342, M.345, C.346, Y.349, K.381 Ligands: POV.5, Y01.40 Ligand excluded by PLIP POV.39: 9 residues within 4Å: Chain C: F.456, M.491 Chain D: F.553, I.557, A.561, I.564 Ligands: Y01.28, POV.31, POV.32 Ligand excluded by PLIP POV.43: 5 residues within 4Å: Chain D: M.435, G.449, V.452 Ligands: POV.11, POV.45 Ligand excluded by PLIP POV.44: 18 residues within 4Å: Chain C: I.341, M.345, I.348, Y.349 Chain D: C.494, W.495, A.498, L.502, Y.509, D.525, Y.526, P.527, L.530 Ligands: Y01.10, POV.11, POV.35, POV.36, PCW.42 Ligand excluded by PLIP POV.45: 3 residues within 4Å: Chain D: F.487 Ligands: Y01.41, POV.43 Ligand excluded by PLIP POV.46: 11 residues within 4Å: Chain D: F.343, C.346, L.386, E.389, L.390, V.393, V.436, T.439, M.440, R.443, M.454 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.12: 5 residues within 4Å: Chain A: D.542 Chain B: D.542 Chain C: D.542 Chain D: D.542 Ligands: CA.13 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Metal complexes: A:D.542, A:D.542, C:D.542, B:D.542, B:D.542 CA.13: 5 residues within 4Å: Chain A: D.542 Chain B: D.542 Chain C: D.542 Chain D: D.542 Ligands: CA.12 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.542, D:D.542, C:D.542, B:D.542

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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