SMTL ID : 7s88.1

Open apo-state cryo-EM structure of human TRPV6 in glyco-diosgenin detergent

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 19 residues within 4Å: Chain A: L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, G.423, P.424, F.425, H.426, I.429, Y.467, R.470 Ligands: PCW.10, POV.12 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.332, A:I.335, A:Y.339, A:Y.339, A:V.391, A:I.394, A:I.398, A:I.399, A:V.402, A:F.425, A:Y.467, A:Y.467 Hydrogen bonds: A:F.425 Salt bridges: A:H.426, A:H.426, A:R.470 Y01.2: 21 residues within 4Å: Chain A: P.424, F.425, L.428, S.455, F.456, V.459, C.463, M.466, R.470, T.479, I.480, Q.483, I.486, F.487, Q.596 Chain B: I.557, T.558, A.561, I.565 Ligands: POV.6, POV.19 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.424, A:F.425, A:L.428, A:F.456, A:F.456, A:V.459, A:I.480, A:I.486, A:F.487, B:I.557, B:A.561, B:I.565 Hydrogen bonds: A:T.479, A:Q.596 Water bridges: A:R.470 Salt bridges: A:R.470 Y01.15: 14 residues within 4Å: Chain A: L.551, F.553, S.556, I.557, A.560, L.568 Chain D: L.490, C.494, M.497, P.527, L.530, F.531, F.534 Ligands: POV.16 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:L.490, D:L.530, D:F.531, D:F.534, D:F.534, D:F.534, D:F.534, A:F.553, A:I.557, A:A.560, A:L.568 Y01.18: 15 residues within 4Å: Chain A: L.490, C.494, M.497, P.527, L.530, F.531, F.534 Chain B: L.551, F.553, S.556, I.557, A.560, I.564, L.568 Ligands: POV.19 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.553, B:I.557, B:A.560, B:I.564, B:L.568, A:L.490, A:L.530, A:F.531, A:F.534, A:F.534, A:F.534, A:F.534 Y01.20: 20 residues within 4Å: Chain B: L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, G.423, P.424, F.425, H.426, I.429, Y.467, R.470, K.607 Ligands: PCW.29, POV.31 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.332, B:I.335, B:Y.339, B:Y.339, B:V.391, B:I.394, B:I.398, B:I.399, B:V.402, B:F.425, B:Y.467, B:Y.467 Hydrogen bonds: B:F.425 Salt bridges: B:H.426, B:H.426, B:R.470 Y01.21: 20 residues within 4Å: Chain B: P.424, F.425, L.428, S.455, F.456, V.459, C.463, M.466, R.470, T.479, Q.483, I.486, F.487, Q.596 Chain C: I.557, T.558, A.561, I.565 Ligands: POV.25, POV.35 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:P.424, B:F.425, B:L.428, B:F.456, B:F.456, B:V.459, B:I.486, B:F.487, C:I.557, C:A.561, C:I.565 Hydrogen bonds: B:T.479, B:Q.596 Water bridges: B:R.470 Salt bridges: B:R.470 Y01.34: 13 residues within 4Å: Chain B: C.494, M.497, P.527, L.530, F.531, F.534 Chain C: L.551, F.553, S.556, I.557, A.560, L.568 Ligands: POV.35 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.530, B:F.534, B:F.534, B:F.534, B:F.534, C:F.553, C:I.557, C:A.560, C:L.568 Y01.36: 19 residues within 4Å: Chain C: L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, G.423, P.424, F.425, H.426, I.429, Y.467, R.470 Ligands: PCW.45, POV.47 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.332, C:I.335, C:Y.339, C:Y.339, C:V.391, C:I.394, C:I.398, C:I.399, C:V.402, C:F.425, C:Y.467, C:Y.467 Hydrogen bonds: C:F.425 Salt bridges: C:H.426, C:H.426, C:R.470 Y01.37: 21 residues within 4Å: Chain C: P.424, F.425, L.428, S.455, F.456, V.459, C.463, M.466, R.470, T.479, I.480, Q.483, I.486, F.487, Q.596 Chain D: I.557, T.558, A.561, I.565 Ligands: POV.41, POV.55 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.424, C:F.425, C:L.428, C:F.456, C:F.456, C:V.459, C:I.480, C:I.486, C:F.487, D:I.557, D:I.565 Hydrogen bonds: C:T.479, C:Q.596 Water bridges: C:R.470 Salt bridges: C:R.470 Y01.54: 13 residues within 4Å: Chain C: C.494, M.497, P.527, L.530, F.531, F.534 Chain D: L.551, F.553, S.556, I.557, A.560, L.568 Ligands: POV.55 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.530, C:F.531, C:F.534, C:F.534, C:F.534, C:F.534, D:F.553, D:I.557, D:A.560, D:L.568 Y01.56: 19 residues within 4Å: Chain D: L.332, I.335, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, G.423, P.424, F.425, H.426, I.429, Y.467, R.470 Ligands: POV.51, PCW.65 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.332, D:I.335, D:Y.339, D:Y.339, D:V.391, D:I.394, D:I.398, D:I.399, D:V.402, D:F.425, D:Y.467, D:Y.467 Hydrogen bonds: D:F.425 Salt bridges: D:H.426, D:H.426, D:R.470 Y01.57: 21 residues within 4Å: Chain A: I.557, T.558, A.561, I.565 Chain D: P.424, F.425, L.428, S.455, F.456, V.459, C.463, M.466, R.470, T.479, I.480, Q.483, I.486, F.487, Q.596 Ligands: POV.16, POV.61 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain D Hydrophobic interactions: A:I.557, A:A.561, A:I.565, D:P.424, D:F.425, D:L.428, D:F.456, D:F.456, D:V.459, D:I.486, D:F.487 Hydrogen bonds: D:T.479, D:Q.596 Water bridges: D:R.470 Salt bridges: D:R.470

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

PCW.3: 6 residues within 4Å: Chain A: W.495 Chain D: F.472, M.474, L.475 Ligands: POV.5, POV.50 Ligand excluded by PLIP PCW.9: 1 residues within 4Å: Ligands: POV.5 Ligand excluded by PLIP PCW.10: 5 residues within 4Å: Chain A: L.332, M.603, L.604, K.607 Ligands: Y01.1 Ligand excluded by PLIP PCW.13: 4 residues within 4Å: Chain A: L.338, I.341, M.345 Ligands: POV.12 Ligand excluded by PLIP PCW.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.22: 6 residues within 4Å: Chain A: F.472, M.474, L.475 Chain B: W.495 Ligands: POV.11, POV.24 Ligand excluded by PLIP PCW.28: 1 residues within 4Å: Ligands: POV.24 Ligand excluded by PLIP PCW.29: 5 residues within 4Å: Chain B: L.332, M.603, L.604, K.607 Ligands: Y01.20 Ligand excluded by PLIP PCW.32: 4 residues within 4Å: Chain B: L.338, M.345, I.384 Ligands: POV.31 Ligand excluded by PLIP PCW.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.38: 6 residues within 4Å: Chain B: F.472, M.474, L.475 Chain C: W.495 Ligands: POV.30, POV.40 Ligand excluded by PLIP PCW.44: 1 residues within 4Å: Ligands: POV.40 Ligand excluded by PLIP PCW.45: 5 residues within 4Å: Chain C: L.332, M.603, L.604, K.607 Ligands: Y01.36 Ligand excluded by PLIP PCW.48: 4 residues within 4Å: Chain C: L.338, I.341, M.345 Ligands: POV.47 Ligand excluded by PLIP PCW.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.52: 4 residues within 4Å: Chain D: L.338, I.341, M.345 Ligands: POV.51 Ligand excluded by PLIP PCW.53: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.58: 6 residues within 4Å: Chain C: F.472, M.474, L.475 Chain D: W.495 Ligands: POV.46, POV.60 Ligand excluded by PLIP PCW.64: 1 residues within 4Å: Ligands: POV.60 Ligand excluded by PLIP PCW.65: 5 residues within 4Å: Chain D: L.332, M.603, L.604, K.607 Ligands: Y01.56 Ligand excluded by PLIP

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

POV.4: 24 residues within 4Å: Chain A: R.350, P.351, D.364, N.365, T.366, Q.369, Q.370, K.371, M.435, V.438, M.442, R.443, S.446, A.447, S.448, G.449, E.450, V.452, M.454, F.456 Chain B: D.550 Ligands: POV.6, POV.8, POV.19 Ligand excluded by PLIP POV.5: 18 residues within 4Å: Chain A: C.494, W.495, A.498, L.502, Y.509, Q.513, D.525, Y.526, P.527, L.530 Chain D: I.341, I.348, Y.349 Ligands: PCW.3, PCW.9, POV.19, POV.50, POV.51 Ligand excluded by PLIP POV.6: 16 residues within 4Å: Chain A: I.420, V.427, L.428, T.431, F.456, Q.483, K.484, I.486, F.487, G.488, R.584 Chain B: A.561, I.564 Ligands: Y01.2, POV.4, POV.19 Ligand excluded by PLIP POV.7: 16 residues within 4Å: Chain A: F.343, C.346, C.347, L.373, Q.374, Y.377, L.386, E.389, T.392, V.393, V.436, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.8: 10 residues within 4Å: Chain A: F.434, M.435, L.437, V.438, M.442, I.445, S.446, A.447, S.448 Ligands: POV.4 Ligand excluded by PLIP POV.11: 16 residues within 4Å: Chain A: R.326, P.327, C.330, G.333, A.334, L.338, V.465, M.466, F.468, A.469, F.472, Q.473 Chain B: W.495, L.496 Ligands: PCW.22, POV.24 Ligand excluded by PLIP POV.12: 12 residues within 4Å: Chain A: I.335, I.341, C.342, M.345, Y.349, K.381, I.384, R.385, G.388 Ligands: Y01.1, PCW.13, POV.24 Ligand excluded by PLIP POV.16: 11 residues within 4Å: Chain A: P.552, F.553, I.557, A.560 Chain D: F.456, M.491 Ligands: Y01.15, Y01.57, POV.59, POV.60, POV.61 Ligand excluded by PLIP POV.19: 13 residues within 4Å: Chain A: V.452, F.456, M.491 Chain B: P.552, F.553, I.557, A.560, A.561 Ligands: Y01.2, POV.4, POV.5, POV.6, Y01.18 Ligand excluded by PLIP POV.23: 23 residues within 4Å: Chain B: R.350, P.351, D.364, N.365, T.366, Q.369, Q.370, K.371, M.435, V.438, M.442, R.443, S.446, A.447, S.448, G.449, E.450, V.452, M.454 Chain C: D.550 Ligands: POV.25, POV.27, POV.35 Ligand excluded by PLIP POV.24: 18 residues within 4Å: Chain A: I.341, I.348, Y.349 Chain B: C.494, W.495, A.498, L.502, Y.509, Q.513, D.525, Y.526, P.527, L.530 Ligands: POV.11, POV.12, PCW.22, PCW.28, POV.35 Ligand excluded by PLIP POV.25: 17 residues within 4Å: Chain B: I.420, L.421, V.427, L.428, T.431, F.456, Q.483, K.484, I.486, F.487, G.488, R.584 Chain C: A.561, I.564 Ligands: Y01.21, POV.23, POV.35 Ligand excluded by PLIP POV.26: 16 residues within 4Å: Chain B: F.343, C.346, C.347, L.373, Q.374, Y.377, L.386, E.389, T.392, V.393, V.436, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.27: 10 residues within 4Å: Chain B: F.434, M.435, L.437, V.438, M.442, I.445, S.446, A.447, S.448 Ligands: POV.23 Ligand excluded by PLIP POV.30: 17 residues within 4Å: Chain B: R.326, P.327, C.330, G.333, A.334, I.335, L.338, V.465, M.466, F.468, A.469, F.472, Q.473 Chain C: W.495, L.496 Ligands: PCW.38, POV.40 Ligand excluded by PLIP POV.31: 13 residues within 4Å: Chain B: I.335, I.341, C.342, M.345, Y.349, K.381, I.384, R.385, G.388, V.391 Ligands: Y01.20, PCW.32, POV.40 Ligand excluded by PLIP POV.35: 11 residues within 4Å: Chain B: F.456, M.491 Chain C: P.552, F.553, I.557, A.560 Ligands: Y01.21, POV.23, POV.24, POV.25, Y01.34 Ligand excluded by PLIP POV.39: 24 residues within 4Å: Chain C: R.350, P.351, D.364, N.365, T.366, Q.369, Q.370, K.371, M.435, V.438, M.442, R.443, S.446, A.447, S.448, G.449, E.450, V.452, M.454, F.456 Chain D: D.550 Ligands: POV.41, POV.43, POV.55 Ligand excluded by PLIP POV.40: 20 residues within 4Å: Chain B: L.337, I.341, I.348, Y.349, V.465 Chain C: C.494, W.495, A.498, L.502, Y.509, Q.513, D.525, Y.526, P.527, L.530 Ligands: POV.30, POV.31, PCW.38, PCW.44, POV.55 Ligand excluded by PLIP POV.41: 16 residues within 4Å: Chain C: I.420, V.427, L.428, T.431, F.456, Q.483, K.484, I.486, F.487, G.488, R.584 Chain D: A.561, I.564 Ligands: Y01.37, POV.39, POV.55 Ligand excluded by PLIP POV.42: 16 residues within 4Å: Chain C: F.343, C.346, C.347, L.373, Q.374, Y.377, L.386, E.389, T.392, V.393, V.436, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.43: 10 residues within 4Å: Chain C: F.434, M.435, L.437, V.438, M.442, I.445, S.446, A.447, S.448 Ligands: POV.39 Ligand excluded by PLIP POV.46: 16 residues within 4Å: Chain C: R.326, P.327, C.330, G.333, A.334, L.338, V.465, M.466, F.468, A.469, F.472, Q.473 Chain D: W.495, L.496 Ligands: PCW.58, POV.60 Ligand excluded by PLIP POV.47: 11 residues within 4Å: Chain C: I.335, I.341, C.342, M.345, Y.349, K.381, R.385, G.388 Ligands: Y01.36, PCW.48, POV.60 Ligand excluded by PLIP POV.50: 16 residues within 4Å: Chain A: W.495, L.496 Chain D: R.326, P.327, C.330, G.333, A.334, L.338, V.465, M.466, F.468, A.469, F.472, Q.473 Ligands: PCW.3, POV.5 Ligand excluded by PLIP POV.51: 12 residues within 4Å: Chain D: I.335, I.341, C.342, M.345, Y.349, K.381, I.384, R.385, G.388 Ligands: POV.5, PCW.52, Y01.56 Ligand excluded by PLIP POV.55: 11 residues within 4Å: Chain C: F.456, M.491 Chain D: P.552, F.553, I.557, A.560 Ligands: Y01.37, POV.39, POV.40, POV.41, Y01.54 Ligand excluded by PLIP POV.59: 24 residues within 4Å: Chain A: D.550 Chain D: R.350, P.351, D.364, N.365, T.366, Q.369, Q.370, K.371, M.435, V.438, M.442, R.443, S.446, A.447, S.448, G.449, E.450, V.452, M.454, F.456 Ligands: POV.16, POV.61, POV.63 Ligand excluded by PLIP POV.60: 18 residues within 4Å: Chain C: I.341, I.348, Y.349 Chain D: C.494, W.495, A.498, L.502, Y.509, Q.513, D.525, Y.526, P.527, L.530 Ligands: POV.16, POV.46, POV.47, PCW.58, PCW.64 Ligand excluded by PLIP POV.61: 16 residues within 4Å: Chain A: A.561, I.564 Chain D: I.420, V.427, L.428, T.431, F.456, Q.483, K.484, I.486, F.487, G.488, R.584 Ligands: POV.16, Y01.57, POV.59 Ligand excluded by PLIP POV.62: 16 residues within 4Å: Chain D: F.343, C.346, C.347, L.373, Q.374, Y.377, L.386, E.389, T.392, V.393, V.436, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.63: 10 residues within 4Å: Chain D: F.434, M.435, L.437, V.438, M.442, I.445, S.446, A.447, S.448 Ligands: POV.59 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.17: 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 B, 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Metal complexes: B:D.542, C:D.542, C:D.542, D:D.542, A:D.542

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuberger, A. et al., Structural mechanisms of TRPV6 inhibition by ruthenium red and econazole. Nat Commun (2021)

Release Date

2021-11-17

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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