SMTL ID : 8ffo.1

Cryo-EM structure of wildtype rabbit TRPV5 with PI(4,5)P2 in nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x ERG: ERGOSTEROL(Non-covalent)

ERG.1: 14 residues within 4Å: Chain A: P.424, F.425, I.428, F.456, V.459, L.460, C.463, M.466, T.479, I.482, Q.483, F.487 Chain D: F.504, A.561 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.425, A:I.428, A:F.456, A:F.456, A:V.459, A:V.459, A:L.460, A:I.482, A:F.487, D:F.504, D:A.561 Hydrogen bonds: A:T.479 ERG.5: 12 residues within 4Å: Chain A: C.494, M.497, A.498, I.501, P.527, L.530, F.531, F.534 Chain D: F.553, C.556, I.557, A.560 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.501, A:P.527, A:L.530, A:F.531, A:F.534, D:I.557, D:A.560 ERG.9: 14 residues within 4Å: Chain A: F.504, A.561 Chain B: P.424, F.425, I.428, F.456, V.459, L.460, C.463, M.466, T.479, I.482, Q.483, F.487 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.425, B:I.428, B:F.456, B:F.456, B:V.459, B:V.459, B:L.460, B:I.482, B:F.487, A:F.504, A:A.561 Hydrogen bonds: B:T.479 ERG.13: 12 residues within 4Å: Chain A: F.553, C.556, I.557, A.560 Chain B: C.494, M.497, A.498, I.501, P.527, L.530, F.531, F.534 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.501, B:P.527, B:L.530, B:F.531, B:F.534, A:I.557, A:A.560 ERG.16: 14 residues within 4Å: Chain B: F.504, A.561 Chain C: P.424, F.425, I.428, F.456, V.459, L.460, C.463, M.466, T.479, I.482, Q.483, F.487 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.425, C:I.428, C:F.456, C:F.456, C:V.459, C:V.459, C:L.460, C:I.482, C:F.487, B:F.504, B:A.561 Hydrogen bonds: C:T.479 ERG.20: 12 residues within 4Å: Chain B: F.553, C.556, I.557, A.560 Chain C: C.494, M.497, A.498, I.501, P.527, L.530, F.531, F.534 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:I.557, B:A.560, C:I.501, C:P.527, C:L.530, C:F.531, C:F.534 ERG.23: 14 residues within 4Å: Chain C: F.504, A.561 Chain D: P.424, F.425, I.428, F.456, V.459, L.460, C.463, M.466, T.479, I.482, Q.483, F.487 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.425, D:I.428, D:F.456, D:F.456, D:V.459, D:V.459, D:L.460, D:I.482, D:F.487, C:F.504, C:A.561 Hydrogen bonds: D:T.479 ERG.27: 12 residues within 4Å: Chain C: F.553, C.556, I.557, A.560 Chain D: C.494, M.497, A.498, I.501, P.527, L.530, F.531, F.534 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.501, D:P.527, D:L.530, D:F.531, D:F.534, C:I.557, C:A.560

16 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.2: 8 residues within 4Å: Chain A: F.343, Y.377, L.386, E.389, T.439, M.440, L.444, L.454 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.343, A:L.386, A:E.389, A:E.389, A:T.439, A:M.440, A:L.444, A:L.454 CPL.3: 8 residues within 4Å: Chain A: C.330, A.333, S.334, I.337, V.465, A.469, F.472 Chain D: L.496 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:A.333, A:I.337, A:A.469, A:F.472, A:F.472, D:L.496 CPL.4: 4 residues within 4Å: Chain A: E.403, H.426, Y.467, M.603 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.467 CPL.7: 13 residues within 4Å: Chain A: I.337, I.341, T.345, I.348, Y.349 Chain D: W.495, A.498, V.499, L.502, H.509, Y.526, P.527, L.530 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:W.495, D:A.498, D:V.499, D:Y.526, D:Y.526, D:L.530, A:I.337, A:I.341, A:I.341 Hydrogen bonds: D:Y.526 CPL.8: 13 residues within 4Å: Chain A: W.495, A.498, V.499, L.502, H.509, Y.526, P.527, L.530 Chain B: I.337, I.341, T.345, I.348, Y.349 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.337, B:I.341, B:I.341, A:W.495, A:A.498, A:V.499, A:Y.526, A:Y.526, A:L.530 Hydrogen bonds: A:Y.526 CPL.10: 8 residues within 4Å: Chain B: F.343, Y.377, L.386, E.389, T.439, M.440, L.444, L.454 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.343, B:L.386, B:E.389, B:E.389, B:T.439, B:M.440, B:L.444, B:L.454 CPL.11: 8 residues within 4Å: Chain A: L.496 Chain B: C.330, A.333, S.334, I.337, V.465, A.469, F.472 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.333, B:I.337, B:A.469, B:F.472, B:F.472, A:L.496 CPL.12: 4 residues within 4Å: Chain B: E.403, H.426, Y.467, M.603 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.467 CPL.15: 13 residues within 4Å: Chain B: W.495, A.498, V.499, L.502, H.509, Y.526, P.527, L.530 Chain C: I.337, I.341, T.345, I.348, Y.349 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:W.495, B:A.498, B:V.499, B:Y.526, B:Y.526, B:L.530, C:I.337, C:I.341, C:I.341 Hydrogen bonds: B:Y.526 CPL.17: 8 residues within 4Å: Chain C: F.343, Y.377, L.386, E.389, T.439, M.440, L.444, L.454 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.343, C:L.386, C:E.389, C:E.389, C:T.439, C:M.440, C:L.444, C:L.454 CPL.18: 8 residues within 4Å: Chain B: L.496 Chain C: C.330, A.333, S.334, I.337, V.465, A.469, F.472 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.333, C:I.337, C:A.469, C:F.472, C:F.472, B:L.496 CPL.19: 4 residues within 4Å: Chain C: E.403, H.426, Y.467, M.603 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.467 CPL.22: 13 residues within 4Å: Chain C: W.495, A.498, V.499, L.502, H.509, Y.526, P.527, L.530 Chain D: I.337, I.341, T.345, I.348, Y.349 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.495, C:A.498, C:V.499, C:Y.526, C:Y.526, C:L.530, D:I.337, D:I.341, D:I.341 Hydrogen bonds: C:Y.526 CPL.24: 8 residues within 4Å: Chain D: F.343, Y.377, L.386, E.389, T.439, M.440, L.444, L.454 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.343, D:L.386, D:E.389, D:E.389, D:T.439, D:M.440, D:L.444, D:L.454 CPL.25: 8 residues within 4Å: Chain C: L.496 Chain D: C.330, A.333, S.334, I.337, V.465, A.469, F.472 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.333, D:I.337, D:A.469, D:F.472, D:F.472, C:L.496 CPL.26: 4 residues within 4Å: Chain D: E.403, H.426, Y.467, M.603 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.467

4 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.6: 9 residues within 4Å: Chain A: R.302, R.305, F.416, G.417, T.419, P.424, K.484, F.487, R.584 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.487, A:F.487 Salt bridges: A:R.302, A:R.305, A:K.484, A:K.484, A:K.484, A:R.584 PIO.14: 9 residues within 4Å: Chain B: R.302, R.305, F.416, G.417, T.419, P.424, K.484, F.487, R.584 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.487, B:F.487 Salt bridges: B:R.302, B:R.305, B:K.484, B:K.484, B:K.484, B:R.584 PIO.21: 9 residues within 4Å: Chain C: R.302, R.305, F.416, G.417, T.419, P.424, K.484, F.487, R.584 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.487, C:F.487 Salt bridges: C:R.302, C:R.305, C:K.484, C:K.484, C:K.484, C:R.584 PIO.28: 9 residues within 4Å: Chain D: R.302, R.305, F.416, G.417, T.419, P.424, K.484, F.487, R.584 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.487, D:F.487 Salt bridges: D:R.302, D:R.305, D:K.484, D:K.484, D:K.484, D:R.584

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, B.H. et al., Structural basis of the activation of TRPV5 channels by long-chain acyl-Coenzyme-A. Nat Commun (2023)

Release Date

2023-11-01

Peptides

Transient receptor potential cation channel subfamily V member 5: 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 5

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