SMTL ID : 7lpa.1

Cryo-EM structure of full-length TRPV1 with capsaicin at 4 degrees Celsius

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.37 Å

Oligo State

homo-tetramer

Ligands

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

LBN.1: 12 residues within 4Å: Chain A: N.437, V.440, Y.444, L.480, S.483, G.484, Y.487, F.488, R.491, E.513, F.516, Y.555 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.444 Hydrogen bonds: A:R.491, A:Y.555 Salt bridges: A:E.513 LBN.7: 4 residues within 4Å: Chain A: I.446, I.447, A.450, Y.454 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.446, A:I.447, A:A.450, A:Y.454 LBN.11: 4 residues within 4Å: Chain B: I.446, I.447, A.450, Y.454 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.446, B:I.447, B:A.450, B:Y.454 LBN.13: 12 residues within 4Å: Chain B: N.437, V.440, Y.444, L.480, S.483, G.484, Y.487, F.488, R.491, E.513, F.516, Y.555 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.444 Hydrogen bonds: B:R.491, B:Y.555 Salt bridges: B:E.513 LBN.18: 4 residues within 4Å: Chain C: I.446, I.447, A.450, Y.454 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.446, C:I.447, C:A.450, C:Y.454 LBN.20: 12 residues within 4Å: Chain C: N.437, V.440, Y.444, L.480, S.483, G.484, Y.487, F.488, R.491, E.513, F.516, Y.555 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.444 Hydrogen bonds: C:R.491, C:Y.555 Salt bridges: C:E.513 LBN.25: 4 residues within 4Å: Chain D: I.446, I.447, A.450, Y.454 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.446, D:I.447, D:A.450, D:Y.454 LBN.27: 12 residues within 4Å: Chain D: N.437, V.440, Y.444, L.480, S.483, G.484, Y.487, F.488, R.491, E.513, F.516, Y.555 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.444 Hydrogen bonds: D:R.491, D:Y.555 Salt bridges: D:E.513

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

6OU.2: 6 residues within 4Å: Chain A: M.581, L.588, Y.631, C.634 Chain D: L.664 Ligands: 6OU.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.588, A:Y.631, D:L.664 6OU.3: 10 residues within 4Å: Chain A: F.589, L.630 Chain B: I.446, T.449, A.450, Y.453, Y.454, W.549 Ligands: 6OU.2, YFP.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.446, B:W.549 Hydrogen bonds: B:Y.454, B:Y.454 6OU.4: 5 residues within 4Å: Chain A: C.578, R.579, F.582 Chain B: Q.561 Ligands: YFP.12 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.561, A:R.579, A:F.582 6OU.6: 9 residues within 4Å: Chain A: I.446, T.449, A.450, Y.453, Y.454, W.549 Chain D: F.589, L.630 Ligands: YFP.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.446, A:W.549 Hydrogen bonds: A:Y.454, A:Y.454 6OU.14: 6 residues within 4Å: Chain A: I.661, L.664 Chain B: L.585, Y.631, C.634 Ligands: 6OU.15 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.585, B:Y.631, A:I.661, A:L.664 6OU.15: 10 residues within 4Å: Chain B: F.589, L.630 Chain C: I.446, T.449, A.450, Y.453, Y.454, W.549 Ligands: 6OU.14, YFP.19 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.446, C:W.549 Hydrogen bonds: C:Y.454, C:Y.454 6OU.16: 5 residues within 4Å: Chain B: C.578, R.579, F.582 Chain C: Q.561 Ligands: YFP.19 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Q.561, B:R.579, B:F.582 6OU.21: 4 residues within 4Å: Chain B: L.664 Chain C: M.581, L.585, Y.631 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.585, C:Y.631 6OU.22: 9 residues within 4Å: Chain C: F.589, L.630 Chain D: I.446, T.449, A.450, Y.453, Y.454, W.549 Ligands: YFP.26 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.446, D:W.549 Hydrogen bonds: D:Y.454, D:Y.454 6OU.23: 5 residues within 4Å: Chain C: C.578, R.579, F.582 Chain D: Q.561 Ligands: YFP.26 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:R.579, C:F.582, D:Q.561 6OU.28: 7 residues within 4Å: Chain C: A.657, I.660, L.664 Chain D: M.581, L.585, Y.631, F.638 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.660, D:L.585, D:Y.631, D:Y.631, D:F.638 6OU.29: 5 residues within 4Å: Chain A: Q.561 Chain D: C.578, R.579, F.582 Ligands: YFP.8 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Q.561, D:R.579, D:F.582

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

4DY.5: 12 residues within 4Å: Chain A: Y.511, S.512, L.515, F.543, T.550, N.551, Y.554, R.557, E.570, I.573 Chain D: L.662, L.669 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.515, D:L.662, D:L.669 Hydrogen bonds: A:R.557 4DY.17: 12 residues within 4Å: Chain A: L.662, L.669 Chain B: Y.511, S.512, L.515, F.543, T.550, N.551, Y.554, R.557, E.570, I.573 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.515, A:L.662, A:L.669 Hydrogen bonds: B:R.557 4DY.24: 12 residues within 4Å: Chain B: L.662, L.669 Chain C: Y.511, S.512, L.515, F.543, T.550, N.551, Y.554, R.557, E.570, I.573 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.515, B:L.662, B:L.669 Hydrogen bonds: C:R.557 4DY.30: 12 residues within 4Å: Chain C: L.662, L.669 Chain D: Y.511, S.512, L.515, F.543, T.550, N.551, Y.554, R.557, E.570, I.573 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.662, C:L.669, D:L.515 Hydrogen bonds: D:R.557

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

YFP.8: 7 residues within 4Å: Chain A: Y.435, F.438, F.559, Q.560 Chain D: F.582 Ligands: 6OU.6, 6OU.29 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.438, A:F.559, A:F.559, A:F.559, D:F.582 YFP.12: 7 residues within 4Å: Chain A: F.582 Chain B: Y.435, F.438, F.559, Q.560 Ligands: 6OU.3, 6OU.4 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.582, B:F.438, B:F.559, B:F.559, B:F.559 YFP.19: 7 residues within 4Å: Chain B: F.582 Chain C: Y.435, F.438, F.559, Q.560 Ligands: 6OU.15, 6OU.16 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.438, C:F.559, C:F.559, C:F.559, B:F.582 YFP.26: 7 residues within 4Å: Chain C: F.582 Chain D: Y.435, F.438, F.559, Q.560 Ligands: 6OU.22, 6OU.23 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.582, D:F.438, D:F.559, D:F.559, D:F.559

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

NA.9: 8 residues within 4Å: Chain A: G.643, M.644 Chain B: G.643, M.644 Chain C: G.643, M.644 Chain D: G.643, M.644 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.643 NA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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