SMTL ID : 7k4a.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: 17 residues within 4Å: Chain A: L.332, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, F.425, H.426, Y.467, R.470, A.599, T.600, M.603 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.332, A:Y.339, A:Y.339, A:V.391, A:I.394, A:I.398, A:I.399, A:V.402, A:Y.467, A:Y.467 Salt bridges: A:H.426, A:R.470 Y01.2: 17 residues within 4Å: Chain A: P.424, F.425, L.428, S.455, F.456, V.459, R.470, T.479, I.480, Q.483, I.486, F.487, Q.596 Chain B: T.558, A.561 Ligands: PCW.4, PCW.20 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.424, A:L.428, A:I.480, A:I.486, A:F.487, B:A.561 Hydrogen bonds: A:Q.596 Salt bridges: A:R.470 Y01.14: 16 residues within 4Å: Chain A: F.553, S.556, A.560, I.564, L.568 Chain D: L.490, C.494, M.497, A.498, I.501, P.527, F.531, F.534, L.538 Ligands: PCW.15, PCW.58 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:F.553, A:A.560, A:I.564, A:I.564, A:L.568, D:L.490, D:A.498, D:I.501, D:P.527, D:F.531, D:F.534, D:L.538 Y01.18: 15 residues within 4Å: Chain A: L.490, C.494, M.497, A.498, P.527, F.531, F.534, L.538 Chain B: F.553, S.556, A.560, I.564, L.568 Ligands: PCW.3, PCW.19 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.490, A:A.498, A:P.527, A:F.531, A:F.534, A:L.538, B:F.553, B:A.560, B:I.564, B:I.564, B:L.568 Y01.21: 17 residues within 4Å: Chain B: L.332, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, F.425, H.426, Y.467, R.470, A.599, T.600, M.603 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.332, B:Y.339, B:Y.339, B:V.391, B:I.394, B:I.398, B:I.399, B:V.402, B:Y.467, B:Y.467 Salt bridges: B:H.426, B:R.470 Y01.22: 18 residues within 4Å: Chain B: P.424, F.425, L.428, S.455, F.456, V.459, R.470, T.479, I.480, Q.483, I.486, F.487, Q.596 Chain C: T.558, A.561, I.565 Ligands: PCW.25, PCW.36 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:A.561, C:I.565, B:P.424, B:L.428, B:I.480, B:I.486, B:F.487 Hydrogen bonds: B:Q.596 Salt bridges: B:R.470 Y01.23: 16 residues within 4Å: Chain B: L.490, C.494, M.497, A.498, I.501, P.527, F.531, F.534, L.538 Chain C: F.553, S.556, A.560, I.564, L.568 Ligands: PCW.24, PCW.35 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.490, B:A.498, B:I.501, B:P.527, B:F.531, B:F.534, B:L.538, C:F.553, C:A.560, C:I.564, C:I.564, C:L.568 Y01.37: 17 residues within 4Å: Chain C: L.332, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, F.425, H.426, Y.467, R.470, A.599, T.600, M.603 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.332, C:Y.339, C:Y.339, C:V.391, C:I.394, C:I.398, C:I.399, C:V.402, C:Y.467, C:Y.467 Salt bridges: C:H.426, C:R.470 Y01.38: 18 residues within 4Å: Chain C: P.424, F.425, L.428, S.455, F.456, V.459, R.470, T.479, I.480, Q.483, I.486, F.487, Q.596 Chain D: T.558, A.561, I.565 Ligands: PCW.41, PCW.55 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.424, C:L.428, C:I.480, C:I.486, C:F.487, D:A.561, D:I.565 Hydrogen bonds: C:Q.596 Salt bridges: C:R.470 Y01.39: 15 residues within 4Å: Chain C: L.490, C.494, M.497, A.498, P.527, F.531, F.534, L.538 Chain D: F.553, S.556, A.560, I.564, L.568 Ligands: PCW.40, PCW.54 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:L.490, C:A.498, C:P.527, C:F.531, C:F.534, C:L.538, D:F.553, D:A.560, D:I.564, D:I.564, D:L.568 Y01.56: 17 residues within 4Å: Chain D: L.332, Y.336, Y.339, V.391, I.394, G.395, I.398, I.399, V.402, E.403, F.425, H.426, Y.467, R.470, A.599, T.600, M.603 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.332, D:Y.339, D:Y.339, D:V.391, D:I.394, D:I.398, D:I.399, D:V.402, D:Y.467, D:Y.467 Salt bridges: D:H.426, D:R.470 Y01.57: 18 residues within 4Å: Chain A: T.558, A.561, I.565 Chain D: P.424, F.425, L.428, S.455, F.456, V.459, R.470, T.479, I.480, Q.483, I.486, F.487, Q.596 Ligands: PCW.16, PCW.59 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:P.424, D:L.428, D:I.480, D:I.486, D:F.487, A:A.561, A:I.565 Hydrogen bonds: D:Q.596 Salt bridges: D:R.470

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

PCW.3: 16 residues within 4Å: Chain A: C.494, W.495, A.498, V.499, Y.509, Q.513, D.525, Y.526, P.527, L.530 Chain D: M.345, I.348, Y.349 Ligands: PCW.8, Y01.18, PCW.19 Ligand excluded by PLIP PCW.4: 4 residues within 4Å: Chain A: P.424, V.427, Q.483 Ligands: Y01.2 Ligand excluded by PLIP PCW.5: 5 residues within 4Å: Chain A: W.495 Chain D: F.472, M.474, L.475 Ligands: PCW.51 Ligand excluded by PLIP PCW.6: 5 residues within 4Å: Chain A: M.435, M.442, G.449, V.452 Ligands: PCW.20 Ligand excluded by PLIP PCW.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.8: 1 residues within 4Å: Ligands: PCW.3 Ligand excluded by PLIP PCW.9: 11 residues within 4Å: Chain A: F.343, C.346, E.375, Y.377, L.386, E.389, T.392, V.393, T.439, M.440, L.444 Ligand excluded by PLIP PCW.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.11: 8 residues within 4Å: Chain A: R.326, G.333, V.465, A.469, F.472, Q.473 Chain B: W.495 Ligands: PCW.26 Ligand excluded by PLIP PCW.12: 2 residues within 4Å: Chain A: M.345, Y.349 Ligand excluded by PLIP PCW.13: 6 residues within 4Å: Chain A: L.338, C.342, M.345, I.384, G.388, V.391 Ligand excluded by PLIP PCW.15: 3 residues within 4Å: Chain A: F.553 Ligands: Y01.14, PCW.58 Ligand excluded by PLIP PCW.16: 5 residues within 4Å: Chain A: F.553, I.557 Chain D: F.456 Ligands: Y01.57, PCW.61 Ligand excluded by PLIP PCW.19: 3 residues within 4Å: Chain B: F.553 Ligands: PCW.3, Y01.18 Ligand excluded by PLIP PCW.20: 5 residues within 4Å: Chain A: F.456 Chain B: F.553, I.557 Ligands: Y01.2, PCW.6 Ligand excluded by PLIP PCW.24: 16 residues within 4Å: Chain A: M.345, I.348, Y.349 Chain B: C.494, W.495, A.498, V.499, Y.509, Q.513, D.525, Y.526, P.527, L.530 Ligands: Y01.23, PCW.29, PCW.35 Ligand excluded by PLIP PCW.25: 4 residues within 4Å: Chain B: P.424, V.427, Q.483 Ligands: Y01.22 Ligand excluded by PLIP PCW.26: 5 residues within 4Å: Chain A: F.472, M.474, L.475 Chain B: W.495 Ligands: PCW.11 Ligand excluded by PLIP PCW.27: 5 residues within 4Å: Chain B: M.435, M.442, G.449, V.452 Ligands: PCW.36 Ligand excluded by PLIP PCW.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.29: 1 residues within 4Å: Ligands: PCW.24 Ligand excluded by PLIP PCW.30: 11 residues within 4Å: Chain B: F.343, C.346, E.375, Y.377, L.386, E.389, T.392, V.393, T.439, M.440, L.444 Ligand excluded by PLIP PCW.31: 1 residues within 4Å: Chain B: L.332 Ligand excluded by PLIP PCW.32: 8 residues within 4Å: Chain B: R.326, G.333, V.465, A.469, F.472, Q.473 Chain C: W.495 Ligands: PCW.42 Ligand excluded by PLIP PCW.33: 2 residues within 4Å: Chain B: M.345, Y.349 Ligand excluded by PLIP PCW.34: 6 residues within 4Å: Chain B: L.338, C.342, M.345, I.384, G.388, V.391 Ligand excluded by PLIP PCW.35: 3 residues within 4Å: Chain C: F.553 Ligands: Y01.23, PCW.24 Ligand excluded by PLIP PCW.36: 5 residues within 4Å: Chain B: F.456 Chain C: F.553, I.557 Ligands: Y01.22, PCW.27 Ligand excluded by PLIP PCW.40: 16 residues within 4Å: Chain B: M.345, I.348, Y.349 Chain C: C.494, W.495, A.498, V.499, Y.509, Q.513, D.525, Y.526, P.527, L.530 Ligands: Y01.39, PCW.45, PCW.54 Ligand excluded by PLIP PCW.41: 4 residues within 4Å: Chain C: P.424, V.427, Q.483 Ligands: Y01.38 Ligand excluded by PLIP PCW.42: 5 residues within 4Å: Chain B: F.472, M.474, L.475 Chain C: W.495 Ligands: PCW.32 Ligand excluded by PLIP PCW.43: 5 residues within 4Å: Chain C: M.435, M.442, G.449, V.452 Ligands: PCW.55 Ligand excluded by PLIP PCW.44: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.45: 1 residues within 4Å: Ligands: PCW.40 Ligand excluded by PLIP PCW.46: 11 residues within 4Å: Chain C: F.343, C.346, E.375, Y.377, L.386, E.389, T.392, V.393, T.439, M.440, L.444 Ligand excluded by PLIP PCW.47: 1 residues within 4Å: Chain C: L.332 Ligand excluded by PLIP PCW.48: 8 residues within 4Å: Chain C: R.326, G.333, V.465, A.469, F.472, Q.473 Chain D: W.495 Ligands: PCW.60 Ligand excluded by PLIP PCW.49: 2 residues within 4Å: Chain C: M.345, Y.349 Ligand excluded by PLIP PCW.50: 6 residues within 4Å: Chain C: L.338, C.342, M.345, I.384, G.388, V.391 Ligand excluded by PLIP PCW.51: 8 residues within 4Å: Chain A: W.495 Chain D: R.326, G.333, V.465, A.469, F.472, Q.473 Ligands: PCW.5 Ligand excluded by PLIP PCW.52: 2 residues within 4Å: Chain D: M.345, Y.349 Ligand excluded by PLIP PCW.53: 5 residues within 4Å: Chain D: L.338, C.342, M.345, I.384, G.388 Ligand excluded by PLIP PCW.54: 4 residues within 4Å: Chain D: F.553 Ligands: Y01.39, PCW.40, PCW.55 Ligand excluded by PLIP PCW.55: 6 residues within 4Å: Chain C: F.456 Chain D: F.553, I.557 Ligands: Y01.38, PCW.43, PCW.54 Ligand excluded by PLIP PCW.58: 16 residues within 4Å: Chain C: M.345, I.348, Y.349 Chain D: C.494, W.495, A.498, V.499, Y.509, Q.513, D.525, Y.526, P.527, L.530 Ligands: Y01.14, PCW.15, PCW.63 Ligand excluded by PLIP PCW.59: 4 residues within 4Å: Chain D: P.424, V.427, Q.483 Ligands: Y01.57 Ligand excluded by PLIP PCW.60: 5 residues within 4Å: Chain C: F.472, M.474, L.475 Chain D: W.495 Ligands: PCW.48 Ligand excluded by PLIP PCW.61: 5 residues within 4Å: Chain D: M.435, M.442, G.449, V.452 Ligands: PCW.16 Ligand excluded by PLIP PCW.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PCW.63: 1 residues within 4Å: Ligands: PCW.58 Ligand excluded by PLIP PCW.64: 11 residues within 4Å: Chain D: F.343, C.346, E.375, Y.377, L.386, E.389, T.392, V.393, T.439, M.440, L.444 Ligand excluded by PLIP PCW.65: 1 residues within 4Å: Chain D: L.332 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 C, 1 interactions with chain B, 1 interactions with chain D, 2 interactions with chain A Metal complexes: C:D.542, B:D.542, D:D.542, A:D.542, A:D.542

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhardwaj, R. et al., Inactivation-mimicking block of the epithelial calcium channel TRPV6. Sci Adv (2020)

Release Date

2020-12-09

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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