SMTL ID : 7lpb.1

Cryo-EM structure of full-length TRPV1 with capsaicin at 25 degrees Celsius

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.54 Å

Oligo State

homo-tetramer

Ligands

8 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.1: 9 residues within 4Å: Chain A: N.437, V.440, G.484, Y.487, F.488, E.513, F.516, Y.554, Y.555 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.513 pi-Cation interactions: A:F.516 LBN.4: 5 residues within 4Å: Chain B: I.447, A.450, Y.454, G.470, F.473 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.447, B:A.450, B:Y.454, B:F.473 LBN.8: 9 residues within 4Å: Chain B: N.437, V.440, G.484, Y.487, F.488, E.513, F.516, Y.554, Y.555 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:E.513 pi-Cation interactions: B:F.516 LBN.11: 5 residues within 4Å: Chain C: I.447, A.450, Y.454, G.470, F.473 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.447, C:A.450, C:Y.454, C:F.473 LBN.15: 9 residues within 4Å: Chain C: N.437, V.440, G.484, Y.487, F.488, E.513, F.516, Y.554, Y.555 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:E.513 pi-Cation interactions: C:F.516 LBN.18: 5 residues within 4Å: Chain D: I.447, A.450, Y.454, G.470, F.473 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.447, D:A.450, D:Y.454, D:F.473, D:F.473 LBN.22: 9 residues within 4Å: Chain D: N.437, V.440, G.484, Y.487, F.488, E.513, F.516, Y.554, Y.555 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:E.513 pi-Cation interactions: D:F.516 LBN.25: 5 residues within 4Å: Chain A: I.447, A.450, Y.454, G.470, F.473 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.447, A:A.450, A:Y.454, A:F.473, A:F.473

12 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.2: 5 residues within 4Å: Chain A: Y.631, C.634 Chain D: I.661, L.664 Ligands: 6OU.3 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.661, D:L.664 6OU.3: 7 residues within 4Å: Chain A: F.582, L.585, F.589, L.630 Chain B: I.446, W.549 Ligands: 6OU.2 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.582, A:L.585, A:F.589, B:I.446, B:W.549 Hydrogen bonds: B:Y.453, B:Y.453 6OU.6: 4 residues within 4Å: Chain A: C.578, R.579 Chain B: Q.561 Ligands: YFP.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.579, B:Q.561 6OU.9: 4 residues within 4Å: Chain A: L.664 Chain B: Y.631, C.634 Ligands: 6OU.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.664 6OU.10: 8 residues within 4Å: Chain B: F.582, L.585, F.589, L.630 Chain C: I.446, Y.454, W.549 Ligands: 6OU.9 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.582, B:L.585, B:F.589, C:I.446, C:W.549 Hydrogen bonds: C:Y.453, C:Y.453 6OU.13: 4 residues within 4Å: Chain B: C.578, R.579 Chain C: Q.561 Ligands: YFP.12 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Q.561, B:R.579 6OU.16: 5 residues within 4Å: Chain B: I.661, L.664 Chain C: Y.631, C.634 Ligands: 6OU.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.661, B:L.664 6OU.17: 8 residues within 4Å: Chain C: F.582, L.585, F.589, L.630 Chain D: I.446, Y.454, W.549 Ligands: 6OU.16 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.446, D:W.549, C:F.582, C:L.585, C:F.589 Hydrogen bonds: D:Y.453, D:Y.453 6OU.20: 4 residues within 4Å: Chain C: C.578, R.579 Chain D: Q.561 Ligands: YFP.19 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:R.579 6OU.23: 5 residues within 4Å: Chain C: I.661, L.664 Chain D: Y.631, C.634 Ligands: 6OU.24 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.661, C:L.664 6OU.24: 8 residues within 4Å: Chain A: I.446, Y.454, W.549 Chain D: F.582, L.585, F.589, L.630 Ligands: 6OU.23 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:F.582, D:L.585, D:F.589, A:I.446, A:W.549 Hydrogen bonds: A:Y.453, A:Y.453 6OU.27: 4 residues within 4Å: Chain A: Q.561 Chain D: C.578, R.579 Ligands: YFP.26 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:R.579

4 x YFP: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol(Non-covalent)

YFP.5: 6 residues within 4Å: Chain B: Y.435, F.438, F.439, F.559, Q.560 Ligands: 6OU.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.438, B:F.439, B:F.559, B:F.559 Hydrogen bonds: B:Q.560 YFP.12: 6 residues within 4Å: Chain C: Y.435, F.438, F.439, F.559, Q.560 Ligands: 6OU.13 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.438, C:F.439, C:F.559, C:F.559 Hydrogen bonds: C:Q.560 YFP.19: 6 residues within 4Å: Chain D: Y.435, F.438, F.439, F.559, Q.560 Ligands: 6OU.20 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.438, D:F.439, D:F.559, D:F.559 Hydrogen bonds: D:G.558, D:Q.560 YFP.26: 6 residues within 4Å: Chain A: Y.435, F.438, F.439, F.559, Q.560 Ligands: 6OU.27 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.438, A:F.439, A:F.559, A:F.559 Hydrogen bonds: A:G.558, A:Q.560

4 x 4DY: (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide(Non-covalent)

4DY.7: 11 residues within 4Å: Chain A: Y.511, S.512, L.515, F.543, A.546, T.550, N.551, Y.554, I.573 Chain D: F.591, L.662 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.515, A:F.543, A:A.546, A:T.550, D:F.591, D:L.662 4DY.14: 11 residues within 4Å: Chain A: F.591, L.662 Chain B: Y.511, S.512, L.515, F.543, A.546, T.550, N.551, Y.554, I.573 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.591, A:L.662, B:L.515, B:F.543, B:A.546, B:T.550 4DY.21: 11 residues within 4Å: Chain B: F.591, L.662 Chain C: Y.511, S.512, L.515, F.543, A.546, T.550, N.551, Y.554, I.573 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.515, C:F.543, C:A.546, C:T.550, B:F.591, B:L.662 4DY.28: 11 residues within 4Å: Chain C: F.591, L.662 Chain D: Y.511, S.512, L.515, F.543, A.546, T.550, N.551, Y.554, I.573 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.515, D:F.543, D:A.546, D:T.550, C:F.591, C:L.662

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, D.H. et al., Heat-dependent opening of TRPV1 in the presence of capsaicin. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-07-28

Peptides

Transient receptor potential cation channel subfamily V member 1: 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 1

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