SMTL ID : 7s89.1

Open apo-state cryo-EM structure of human TRPV6 in cNW11 nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 21 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, E.403, G.423, P.424, F.425, H.426, I.429, Y.467, R.470, K.607 Ligands: Y01.2, POV.10 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.332, A:I.335, A:Y.336, A:Y.339, A:Y.339, A:V.391, A:I.394, A:I.398, A:I.399, A:V.402, A:E.403, A:H.426, A:Y.467, A:Y.467 Hydrogen bonds: A:F.425, A:H.426 Salt bridges: A:R.470 Y01.2: 21 residues within 4Å: Chain A: P.424, F.425, S.455, F.456, V.459, C.463, M.466, R.470, T.479, I.480, I.482, Q.483, I.486, Q.596 Chain B: M.554, I.557, T.558, A.561, I.565 Ligands: Y01.1, POV.6 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.424, A:F.456, A:V.459, A:I.480, A:I.482, A:Q.483, A:I.486, B:I.557, B:I.565 Hydrogen bonds: A:Q.596 Salt bridges: A:R.470 Y01.11: 13 residues within 4Å: Chain A: L.551, F.553, S.556, A.560 Chain D: L.490, C.494, M.497, P.527, L.530, F.531, F.534 Ligands: POV.12, POV.43 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:F.553, A:A.560, D:L.490, D:M.497, D:F.531, D:F.534, D:F.534, D:F.534 Y01.14: 13 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, A.560 Ligands: POV.4, POV.15 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.490, A:M.497, A:F.531, A:F.531, A:F.534, A:F.534, A:F.534, B:F.553, B:A.560 Y01.16: 21 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, E.403, G.423, P.424, F.425, H.426, I.429, Y.467, R.470, K.607 Ligands: Y01.17, POV.24 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.332, B:I.335, B:Y.336, B:Y.339, B:Y.339, B:V.391, B:I.394, B:I.398, B:I.399, B:V.402, B:E.403, B:H.426, B:Y.467, B:Y.467 Hydrogen bonds: B:F.425, B:H.426 Salt bridges: B:R.470 Y01.17: 21 residues within 4Å: Chain B: P.424, F.425, S.455, F.456, V.459, C.463, M.466, R.470, T.479, I.480, I.482, Q.483, I.486, Q.596 Chain C: M.554, I.557, T.558, A.561, I.565 Ligands: Y01.16, POV.20 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.424, B:F.456, B:V.459, B:I.480, B:I.482, B:Q.483, B:I.486, C:I.557, C:I.565 Hydrogen bonds: B:Q.596 Salt bridges: B:R.470 Y01.25: 13 residues within 4Å: Chain B: L.490, C.494, M.497, P.527, L.530, F.531, F.534 Chain C: L.551, F.553, S.556, A.560 Ligands: POV.19, POV.26 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.490, B:M.497, B:F.531, B:F.531, B:F.534, B:F.534, B:F.534, C:F.553, C:A.560 Y01.27: 21 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, E.403, G.423, P.424, F.425, H.426, I.429, Y.467, R.470, K.607 Ligands: Y01.28, POV.35 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.332, C:I.335, C:Y.336, C:Y.339, C:Y.339, C:V.391, C:I.394, C:I.398, C:I.399, C:V.402, C:E.403, C:H.426, C:Y.467, C:Y.467 Hydrogen bonds: C:F.425, C:H.426 Salt bridges: C:R.470 Y01.28: 22 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, I.482, Q.483, I.486, Q.596 Chain D: M.554, I.557, T.558, A.561, I.565 Ligands: Y01.27, POV.31 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.424, C:L.428, C:F.456, C:V.459, C:I.480, C:I.482, C:Q.483, C:I.486, D:I.557, D:I.565 Hydrogen bonds: C:Q.596 Salt bridges: C:R.470 Y01.38: 13 residues within 4Å: Chain C: L.490, C.494, M.497, P.527, L.530, F.531, F.534 Chain D: L.551, F.553, S.556, A.560 Ligands: POV.30, POV.39 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.490, C:M.497, C:F.531, C:F.534, C:F.534, C:F.534, D:F.553, D:A.560 Y01.40: 21 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, E.403, G.423, P.424, F.425, H.426, I.429, Y.467, R.470, K.607 Ligands: POV.37, Y01.41 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.332, D:I.335, D:Y.336, D:Y.339, D:Y.339, D:V.391, D:I.394, D:I.398, D:I.399, D:V.402, D:E.403, D:H.426, D:Y.467, D:Y.467 Hydrogen bonds: D:F.425, D:H.426 Salt bridges: D:R.470 Y01.41: 22 residues within 4Å: Chain A: M.554, 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, I.482, Q.483, I.486, Q.596 Ligands: Y01.40, POV.44 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:P.424, D:L.428, D:F.456, D:V.459, D:I.480, D:I.482, D:Q.483, D:I.486, A:I.557, A:I.565 Hydrogen bonds: D:Q.596 Salt bridges: D:R.470

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

POV.3: 8 residues within 4Å: Chain A: M.435, V.438, M.442, S.448, G.449, V.452, P.453 Ligands: POV.15 Ligand excluded by PLIP POV.4: 16 residues within 4Å: Chain A: W.495, A.498, L.502, Y.509, D.525, Y.526, P.527, L.530 Chain D: I.341, M.345, I.348, Y.349, W.462 Ligands: POV.5, Y01.14, POV.37 Ligand excluded by PLIP POV.5: 13 residues within 4Å: Chain A: W.495, L.496 Chain D: P.327, C.330, M.331, G.333, A.334, V.465, M.466, F.468, A.469 Ligands: POV.4, PCW.36 Ligand excluded by PLIP POV.6: 7 residues within 4Å: Chain A: P.424, L.428, T.431, F.456, L.460, F.487 Ligands: Y01.2 Ligand excluded by PLIP POV.7: 15 residues within 4Å: Chain A: F.343, C.346, C.347, L.373, 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.9: 13 residues within 4Å: Chain A: P.327, C.330, M.331, G.333, A.334, V.465, M.466, F.468, A.469 Chain B: W.495, L.496 Ligands: PCW.8, POV.19 Ligand excluded by PLIP POV.10: 13 residues within 4Å: Chain A: I.335, L.338, C.342, M.345, C.346, Y.349, K.381, I.384, R.385, G.388, V.391 Ligands: Y01.1, POV.19 Ligand excluded by PLIP POV.12: 9 residues within 4Å: Chain A: P.552, F.553, I.557, A.561, I.564 Chain D: V.452, F.456 Ligands: Y01.11, POV.42 Ligand excluded by PLIP POV.15: 9 residues within 4Å: Chain A: V.452, F.456 Chain B: P.552, F.553, I.557, A.561, I.564 Ligands: POV.3, Y01.14 Ligand excluded by PLIP POV.18: 8 residues within 4Å: Chain B: M.435, V.438, M.442, S.448, G.449, V.452, P.453 Ligands: POV.26 Ligand excluded by PLIP POV.19: 16 residues within 4Å: Chain A: I.341, M.345, I.348, Y.349, W.462 Chain B: W.495, A.498, L.502, Y.509, D.525, Y.526, P.527, L.530 Ligands: POV.9, POV.10, Y01.25 Ligand excluded by PLIP POV.20: 8 residues within 4Å: Chain B: P.424, L.428, T.431, M.435, F.456, L.460, F.487 Ligands: Y01.17 Ligand excluded by PLIP POV.21: 15 residues within 4Å: Chain B: F.343, C.346, C.347, L.373, 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.23: 14 residues within 4Å: Chain B: P.327, C.330, M.331, G.333, A.334, V.465, M.466, F.468, A.469 Chain C: W.495, L.496, V.499 Ligands: PCW.22, POV.30 Ligand excluded by PLIP POV.24: 13 residues within 4Å: Chain B: I.335, L.338, C.342, M.345, C.346, Y.349, K.381, I.384, R.385, G.388, V.391 Ligands: Y01.16, POV.30 Ligand excluded by PLIP POV.26: 9 residues within 4Å: Chain B: V.452, F.456 Chain C: P.552, F.553, I.557, A.561, I.564 Ligands: POV.18, Y01.25 Ligand excluded by PLIP POV.29: 8 residues within 4Å: Chain C: M.435, V.438, M.442, S.448, G.449, V.452, P.453 Ligands: POV.39 Ligand excluded by PLIP POV.30: 16 residues within 4Å: Chain B: I.341, M.345, I.348, Y.349, W.462 Chain C: W.495, A.498, L.502, Y.509, D.525, Y.526, P.527, L.530 Ligands: POV.23, POV.24, Y01.38 Ligand excluded by PLIP POV.31: 8 residues within 4Å: Chain C: P.424, L.428, T.431, M.435, F.456, L.460, F.487 Ligands: Y01.28 Ligand excluded by PLIP POV.32: 15 residues within 4Å: Chain C: F.343, C.346, C.347, L.373, 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.34: 14 residues within 4Å: Chain C: P.327, C.330, M.331, G.333, A.334, V.465, M.466, F.468, A.469 Chain D: W.495, L.496, V.499 Ligands: PCW.33, POV.43 Ligand excluded by PLIP POV.35: 13 residues within 4Å: Chain C: I.335, L.338, C.342, M.345, C.346, Y.349, K.381, I.384, R.385, G.388, V.391 Ligands: Y01.27, POV.43 Ligand excluded by PLIP POV.37: 13 residues within 4Å: Chain D: I.335, L.338, C.342, M.345, C.346, Y.349, K.381, I.384, R.385, G.388, V.391 Ligands: POV.4, Y01.40 Ligand excluded by PLIP POV.39: 9 residues within 4Å: Chain C: V.452, F.456 Chain D: P.552, F.553, I.557, A.561, I.564 Ligands: POV.29, Y01.38 Ligand excluded by PLIP POV.42: 8 residues within 4Å: Chain D: M.435, V.438, M.442, S.448, G.449, V.452, P.453 Ligands: POV.12 Ligand excluded by PLIP POV.43: 17 residues within 4Å: Chain C: I.341, M.345, I.348, Y.349, W.462 Chain D: W.495, A.498, L.502, Y.509, D.525, Y.526, P.527, L.530 Ligands: Y01.11, PCW.33, POV.34, POV.35 Ligand excluded by PLIP POV.44: 8 residues within 4Å: Chain D: P.424, L.428, T.431, M.435, F.456, L.460, F.487 Ligands: Y01.41 Ligand excluded by PLIP POV.45: 15 residues within 4Å: Chain D: F.343, C.346, C.347, L.373, 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

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

PCW.8: 5 residues within 4Å: Chain A: F.472, M.474, L.475 Chain B: W.495 Ligands: POV.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.472, A:M.474, A:L.475 PCW.22: 5 residues within 4Å: Chain B: F.472, M.474, L.475 Chain C: W.495 Ligands: POV.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.472, B:M.474, B:L.475 PCW.33: 6 residues within 4Å: Chain C: F.472, M.474, L.475 Chain D: W.495 Ligands: POV.34, POV.43 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.472, C:M.474, C:L.475 PCW.36: 5 residues within 4Å: Chain A: W.495 Chain D: F.472, M.474, L.475 Ligands: POV.5 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.472, D:M.474, D:L.475

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 4 residues within 4Å: Chain A: D.542 Chain B: D.542 Chain C: D.542 Chain D: D.542 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Metal complexes: B:D.542, A:D.542, A:D.542, C:D.542, C:D.542, D: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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