SMTL ID : 7s8b.1

Cryo-EM structure of human TRPV6 in complex with channel blocker ruthenium red

Coordinates

PDB Format

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, Y.339, V.391, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, I.429, Y.467, R.470, M.603, K.607 19 PLIP interactions: 19 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:V.391, A:I.398, A:I.399, A:V.402, A:E.403, A:F.425, A:I.429, A:Y.467, A:Y.467 Hydrogen bonds: A:F.425 Salt bridges: A:H.426, A:H.426, A:R.470 Y01.2: 20 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, I.482, Q.483, I.486, Q.596 Chain B: I.557, T.558, A.561, I.565 Ligands: POV.15 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.424, A:P.424, A:F.425, A:F.425, A:V.459, A:Q.483, A:I.486, B:I.557, B:T.558, B:I.565 Hydrogen bonds: A:Q.483, A:Q.596 Salt bridges: A:R.470 Y01.10: 16 residues within 4Å: Chain A: D.550, L.551, F.553, S.556, I.557, I.564 Chain D: C.494, M.497, A.498, Y.524, P.527, L.530, F.531, F.534 Ligands: POV.11, POV.33 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:I.557, A:I.564, D:A.498, D:P.527, D:F.531, D:F.534 Hydrogen bonds: A:D.550, D:Y.524 Y01.14: 16 residues within 4Å: Chain A: C.494, M.497, A.498, Y.524, P.527, L.530, F.531, F.534 Chain B: D.550, L.551, F.553, S.556, I.557, I.564 Ligands: POV.15, POV.36 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.498, A:P.527, A:F.531, A:F.534, B:I.557, B:I.564 Hydrogen bonds: A:Y.524, B:D.550 Y01.16: 17 residues within 4Å: Chain B: L.332, I.335, Y.339, V.391, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, I.429, Y.467, R.470, M.603, K.607 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.332, B:L.332, B:I.335, B:Y.339, B:Y.339, B:V.391, B:I.398, B:I.399, B:V.402, B:E.403, B:F.425, B:I.429, B:Y.467, B:Y.467 Hydrogen bonds: 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, L.428, V.459, C.463, M.466, T.479, I.480, I.482, Q.483, I.486, F.487, Q.596 Chain C: I.557, A.561, I.565 Ligands: POV.26 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:P.424, B:F.425, B:F.425, B:V.459, B:Q.483, B:I.486, B:F.487, C:I.557, C:A.561, C:I.565 Hydrogen bonds: B:Q.483, B:Q.596 Salt bridges: B:R.470 Y01.25: 16 residues within 4Å: Chain B: C.494, M.497, A.498, Y.524, P.527, L.530, F.531, F.534 Chain C: D.550, L.551, F.553, S.556, I.557, I.564 Ligands: POV.7, POV.26 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.498, B:P.527, B:F.531, B:F.534, C:F.553, C:I.557, C:I.564 Hydrogen bonds: B:Y.524, C:D.550 Y01.27: 18 residues within 4Å: Chain C: L.332, I.335, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, I.429, Y.467, R.470, M.603, K.607 18 PLIP interactions: 18 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:E.403, C:F.425, C:I.429, C:Y.467, C:Y.467 Hydrogen bonds: C:F.425 Salt bridges: C:H.426, C:H.426, C:R.470 Y01.28: 21 residues within 4Å: Chain C: P.424, F.425, L.428, F.456, V.459, L.460, C.463, M.466, R.470, T.479, I.480, I.482, Q.483, F.487, Q.596 Chain D: F.504, I.557, T.558, A.561, I.565 Ligands: POV.40 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:P.424, C:F.425, C:F.425, C:F.425, C:L.428, C:V.459, C:V.459, C:L.460, C:Q.483, C:F.487, D:F.504, D:I.557, D:A.561 Hydrogen bonds: C:Q.483, C:Q.596 Salt bridges: C:R.470 Y01.39: 16 residues within 4Å: Chain C: C.494, M.497, A.498, Y.524, P.527, L.530, F.531, F.534 Chain D: D.550, L.551, F.553, S.556, I.557, I.564 Ligands: POV.22, POV.40 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:I.557, D:I.564, C:A.498, C:P.527, C:F.531, C:F.534 Hydrogen bonds: D:D.550, C:Y.524 Y01.41: 17 residues within 4Å: Chain D: L.332, I.335, Y.339, V.391, G.395, I.398, I.399, V.402, E.403, G.423, F.425, H.426, I.429, Y.467, R.470, M.603, K.607 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:L.332, D:L.332, D:I.335, D:Y.339, D:Y.339, D:V.391, D:I.398, D:I.399, D:V.402, D:E.403, D:F.425, D:I.429, D:Y.467, D:Y.467 Hydrogen bonds: D:F.425 Salt bridges: D:H.426, D:H.426, D:R.470 Y01.42: 19 residues within 4Å: Chain A: I.557, T.558, A.561, I.565 Chain D: P.424, F.425, L.428, S.455, V.459, C.463, M.466, R.470, T.479, I.480, I.482, Q.483, I.486, Q.596 Ligands: POV.11 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:P.424, D:P.424, D:F.425, D:F.425, D:L.428, D:V.459, D:Q.483, D:I.486, A:I.557 Hydrogen bonds: D:Q.483, 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: W.495 Chain D: F.472, Q.473, M.474, L.475 Ligands: POV.37 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:W.495, A:W.495, D:F.472, D:F.472, D:L.475 PCW.18: 6 residues within 4Å: Chain A: F.472, Q.473, M.474, L.475 Chain B: W.495 Ligands: POV.8 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.472, A:F.472, A:L.475, B:W.495, B:W.495 PCW.29: 6 residues within 4Å: Chain B: F.472, Q.473, M.474, L.475 Chain C: W.495 Ligands: POV.23 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.472, B:F.472, B:L.475, C:W.495, C:W.495 PCW.43: 6 residues within 4Å: Chain C: F.472, Q.473, M.474, L.475 Chain D: W.495 Ligands: POV.34 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.495, D:W.495, C:F.472, C:F.472, C:F.472, 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, S.448, G.449, P.453 Ligands: POV.15 Ligand excluded by PLIP POV.5: 12 residues within 4Å: Chain A: C.346, C.347, L.373, Y.377, L.386, E.389, V.393, V.436, T.439, R.443, L.444, M.454 Ligand excluded by PLIP POV.6: 3 residues within 4Å: Chain A: V.441, I.445, A.447 Ligand excluded by PLIP POV.7: 18 residues within 4Å: Chain A: I.341, T.344, M.345, I.348, Y.349, W.462, V.465 Chain B: W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527 Ligands: POV.8, POV.9, Y01.25 Ligand excluded by PLIP POV.8: 17 residues within 4Å: Chain A: K.322, R.326, P.327, C.330, M.331, G.333, A.334, V.465, M.466, A.469, F.472, L.475 Chain B: W.495, L.496, V.499 Ligands: POV.7, PCW.18 Ligand excluded by PLIP POV.9: 11 residues within 4Å: Chain A: I.341, C.342, M.345, C.346, Y.349, K.381, I.384, R.385, V.387, V.391 Ligands: POV.7 Ligand excluded by PLIP POV.11: 7 residues within 4Å: Chain A: F.553, I.557, I.564 Chain D: F.456 Ligands: Y01.10, Y01.42, POV.44 Ligand excluded by PLIP POV.15: 7 residues within 4Å: Chain A: F.456 Chain B: F.553, I.557, I.564 Ligands: Y01.2, POV.4, Y01.14 Ligand excluded by PLIP POV.19: 5 residues within 4Å: Chain B: M.435, S.448, G.449, P.453 Ligands: POV.26 Ligand excluded by PLIP POV.20: 11 residues within 4Å: Chain B: C.346, L.373, Y.377, L.386, E.389, V.393, V.436, T.439, R.443, L.444, M.454 Ligand excluded by PLIP POV.21: 3 residues within 4Å: Chain B: V.441, I.445, A.447 Ligand excluded by PLIP POV.22: 18 residues within 4Å: Chain B: I.341, T.344, M.345, I.348, Y.349, W.462, V.465 Chain C: W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527 Ligands: POV.23, POV.24, Y01.39 Ligand excluded by PLIP POV.23: 17 residues within 4Å: Chain B: K.322, R.326, P.327, C.330, M.331, G.333, A.334, V.465, M.466, A.469, F.472, L.475 Chain C: W.495, L.496, V.499 Ligands: POV.22, PCW.29 Ligand excluded by PLIP POV.24: 11 residues within 4Å: Chain B: I.341, C.342, M.345, C.346, Y.349, K.381, I.384, R.385, V.387, V.391 Ligands: POV.22 Ligand excluded by PLIP POV.26: 7 residues within 4Å: Chain B: F.456 Chain C: F.553, I.557, I.564 Ligands: Y01.17, POV.19, Y01.25 Ligand excluded by PLIP POV.30: 5 residues within 4Å: Chain C: M.435, S.448, G.449, P.453 Ligands: POV.40 Ligand excluded by PLIP POV.31: 12 residues within 4Å: Chain C: C.346, L.373, Y.377, L.386, E.389, V.393, V.436, T.439, M.440, R.443, L.444, M.454 Ligand excluded by PLIP POV.32: 3 residues within 4Å: Chain C: V.441, I.445, A.447 Ligand excluded by PLIP POV.33: 18 residues within 4Å: Chain C: I.341, T.344, M.345, I.348, Y.349, W.462, V.465 Chain D: W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527 Ligands: Y01.10, POV.34, POV.35 Ligand excluded by PLIP POV.34: 17 residues within 4Å: Chain C: K.322, R.326, P.327, C.330, M.331, G.333, A.334, V.465, M.466, A.469, F.472, L.475 Chain D: W.495, L.496, V.499 Ligands: POV.33, PCW.43 Ligand excluded by PLIP POV.35: 13 residues within 4Å: Chain C: L.338, I.341, C.342, M.345, C.346, Y.349, K.381, I.384, R.385, V.387, G.388, V.391 Ligands: POV.33 Ligand excluded by PLIP POV.36: 18 residues within 4Å: Chain A: W.495, A.498, V.499, L.502, Y.509, D.525, Y.526, P.527 Chain D: I.341, T.344, M.345, I.348, Y.349, W.462, V.465 Ligands: Y01.14, POV.37, POV.38 Ligand excluded by PLIP POV.37: 17 residues within 4Å: Chain A: W.495, L.496, V.499 Chain D: K.322, R.326, P.327, C.330, M.331, G.333, A.334, V.465, M.466, A.469, F.472, L.475 Ligands: PCW.3, POV.36 Ligand excluded by PLIP POV.38: 11 residues within 4Å: Chain D: I.341, C.342, M.345, C.346, Y.349, K.381, I.384, R.385, V.387, V.391 Ligands: POV.36 Ligand excluded by PLIP POV.40: 7 residues within 4Å: Chain C: F.456 Chain D: F.553, I.557, I.564 Ligands: Y01.28, POV.30, Y01.39 Ligand excluded by PLIP POV.44: 5 residues within 4Å: Chain D: M.435, S.448, G.449, P.453 Ligands: POV.11 Ligand excluded by PLIP POV.45: 12 residues within 4Å: Chain D: C.346, C.347, L.373, Y.377, L.386, E.389, V.393, V.436, T.439, R.443, L.444, M.454 Ligand excluded by PLIP POV.46: 3 residues within 4Å: Chain D: V.441, I.445, A.447 Ligand excluded by PLIP

1 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: R2R.13 No protein-ligand interaction detected (PLIP)

1 x R2R: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)(Non-covalent)

R2R.13: 13 residues within 4Å: Chain A: T.539, I.541, D.542 Chain B: T.539, I.541, D.542 Chain C: T.539, I.541, D.542 Chain D: T.539, I.541, D.542 Ligands: CA.12 20 PLIP interactions: 4 interactions with chain D, 6 interactions with chain B, 4 interactions with chain C, 6 interactions with chain A Hydrogen bonds: D:T.539, D:T.539, D:T.539, D:D.542, B:T.539, B:T.539, B:T.539, B:D.542, B:D.542, B:D.542, C:T.539, C:T.539, C:T.539, C:D.542, A:T.539, A:T.539, A:T.539, A:D.542, A: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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