SMTL ID : 7l2h.1

Cryo-EM structure of unliganded full-length TRPV1 at neutral pH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x XJ7: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate(Non-covalent)

XJ7.1: 16 residues within 4Å: Chain A: R.413, D.513, S.514, Y.515, S.516, L.519, F.547, M.551, T.554, L.557, Y.558, R.561, E.574, L.703, Q.704, I.707 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.515, A:F.547, A:L.557 Hydrogen bonds: A:R.413, A:R.413, A:S.514, A:Y.515, A:S.516, A:S.516, A:Q.704 Salt bridges: A:R.561 XJ7.4: 14 residues within 4Å: Chain B: H.414, D.513, S.514, Y.515, S.516, L.519, F.547, T.554, Y.558, R.561, E.574, L.703, Q.704, I.707 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.547 Hydrogen bonds: B:R.413, B:H.414, B:Y.515, B:S.516, B:S.516, B:Q.704 Salt bridges: B:R.561 XJ7.6: 16 residues within 4Å: Chain A: F.595 Chain C: R.413, D.513, S.514, Y.515, S.516, L.519, F.547, M.551, T.554, Y.558, R.561, E.574, L.703, Q.704, I.707 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.547, A:F.595 Hydrogen bonds: C:R.413, C:R.413, C:Y.515, C:S.516, C:S.516, C:Q.704 Salt bridges: C:R.561 XJ7.8: 16 residues within 4Å: Chain D: R.413, H.414, D.513, Y.515, S.516, L.519, F.547, M.551, T.554, L.557, Y.558, R.561, E.574, L.703, Q.704, I.707 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.547, D:L.557 Hydrogen bonds: D:R.413, D:R.413, D:Y.515, D:S.516, D:Q.704 Salt bridges: D:R.561

4 x XJD: (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl tridecanoate(Non-covalent)

XJD.2: 9 residues within 4Å: Chain A: L.589, L.592, S.633, Y.635, C.638, F.642 Chain B: I.664, I.665, L.668 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.589, A:L.592, A:Y.635, A:Y.635, A:F.642, B:I.664, B:I.665, B:L.668 Hydrogen bonds: A:S.633 XJD.5: 9 residues within 4Å: Chain B: L.589, L.592, S.633, Y.635, C.638, F.642 Chain D: I.664, I.665, L.668 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:L.589, B:L.592, B:Y.635, B:Y.635, B:F.642, D:I.664, D:I.665, D:L.668 Hydrogen bonds: B:S.633 XJD.7: 9 residues within 4Å: Chain A: I.664, I.665, L.668 Chain C: L.589, L.592, S.633, Y.635, C.638, F.642 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.589, C:L.592, C:Y.635, C:Y.635, C:F.642, A:I.664, A:I.665, A:L.668 Hydrogen bonds: C:S.633 Salt bridges: A:K.660 XJD.9: 9 residues within 4Å: Chain C: K.660, I.664, I.665, L.668 Chain D: L.592, S.633, Y.635, C.638, F.642 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.664, C:I.665, C:L.668, D:L.592, D:Y.635, D:Y.635, D:F.642 Salt bridges: C:K.660, C:K.660 Hydrogen bonds: D:S.633

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 8 residues within 4Å: Chain A: G.647, M.648 Chain B: G.647, M.648 Chain C: G.647, M.648 Chain D: G.647, M.648 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.647

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, K. et al., Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. Cell (2021)

Release Date

2021-09-22

Peptides

Transient receptor potential cation channel subfamily V member 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily V member 1

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