SMTL ID : 7rqw.1

Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in an open state, class III

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.1: 30 residues within 4Å: Chain A: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, A.566, I.569, E.570, I.573, L.574, L.577 Chain C: F.587, F.591, L.662, A.665, I.668, L.669 Ligands: 6OU.4, 6OU.13 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:F.591, C:F.591, C:L.669, C:L.669, A:Y.511, A:I.514, A:L.515, A:L.515, A:A.546, A:A.566, A:I.573 Hydrogen bonds: A:Y.511 pi-Stacking: A:Y.511 6EU.7: 30 residues within 4Å: Chain B: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, A.566, I.569, E.570, I.573, L.574, L.577 Chain D: F.587, F.591, L.662, A.665, I.668, L.669 Ligands: 6OU.10, 6OU.17 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:Y.511, B:I.514, B:L.515, B:L.515, B:A.546, B:A.566, B:I.573, D:F.591, D:F.591, D:L.669, D:L.669 Hydrogen bonds: B:Y.511 pi-Stacking: B:Y.511 6EU.14: 30 residues within 4Å: Chain B: F.587, F.591, L.662, A.665, I.668, L.669 Chain C: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, A.566, I.569, E.570, I.573, L.574, L.577 Ligands: 6OU.11, 6OU.16 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Y.511, C:I.514, C:L.515, C:L.515, C:A.546, C:A.566, C:I.573, B:F.591, B:F.591, B:L.669, B:L.669 Hydrogen bonds: C:Y.511 pi-Stacking: C:Y.511 6EU.18: 30 residues within 4Å: Chain A: F.587, F.591, L.662, A.665, I.668, L.669 Chain D: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, F.522, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, A.566, I.569, E.570, I.573, L.574, L.577 Ligands: 6OU.6, 6OU.20 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:Y.511, D:I.514, D:L.515, D:L.515, D:A.546, D:A.566, D:I.573, A:F.591, A:F.591, A:L.669, A:L.669 Hydrogen bonds: D:Y.511 pi-Stacking: D:Y.511

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

PCW.2: 17 residues within 4Å: Chain A: F.436, N.437, V.440, Y.441, Y.444, I.447, L.480, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.444, A:Y.444, A:I.447, A:L.480 Hydrogen bonds: A:N.437, A:Y.487 Salt bridges: A:E.513 PCW.8: 17 residues within 4Å: Chain B: F.436, N.437, V.440, Y.441, Y.444, I.447, L.480, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.444, B:Y.444, B:I.447, B:L.480 Hydrogen bonds: B:N.437, B:Y.487 Salt bridges: B:E.513 PCW.15: 17 residues within 4Å: Chain C: F.436, N.437, V.440, Y.441, Y.444, I.447, L.480, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.444, C:Y.444, C:I.447, C:L.480 Hydrogen bonds: C:N.437, C:Y.487 Salt bridges: C:E.513 PCW.19: 17 residues within 4Å: Chain D: F.436, N.437, V.440, Y.441, Y.444, I.447, L.480, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.444, D:Y.444, D:I.447, D:L.480 Hydrogen bonds: D:N.437, D:Y.487 Salt bridges: D:E.513

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

LBN.3: 14 residues within 4Å: Chain A: E.600 Chain D: L.443, I.446, I.447, A.450, A.451, Y.453, Y.454, G.470, F.473, R.474, T.476, G.477, L.480 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Salt bridges: A:E.600 Hydrophobic interactions: D:I.446, D:A.450, D:Y.454 LBN.5: 14 residues within 4Å: Chain A: L.443, I.446, I.447, A.450, A.451, Y.453, Y.454, G.470, F.473, R.474, T.476, G.477, L.480 Chain C: E.600 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.446, A:A.450, A:Y.454 Salt bridges: C:E.600 LBN.9: 14 residues within 4Å: Chain B: E.600 Chain C: L.443, I.446, I.447, A.450, A.451, Y.453, Y.454, G.470, F.473, R.474, T.476, G.477, L.480 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.446, C:A.450, C:Y.454 Salt bridges: B:E.600 LBN.12: 14 residues within 4Å: Chain B: L.443, I.446, I.447, A.450, A.451, Y.453, Y.454, G.470, F.473, R.474, T.476, G.477, L.480 Chain D: E.600 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:I.446, B:A.450, B:Y.454 Salt bridges: D:E.600

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

6OU.4: 10 residues within 4Å: Chain A: K.504, F.507, V.508, I.573, L.574, R.575, L.577, C.578, F.582 Ligands: 6EU.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.507, A:L.574, A:L.577 6OU.6: 15 residues within 4Å: Chain A: F.649, K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain D: L.588, Y.631, S.632, C.634, L.635, F.638 Ligands: 6EU.18 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:A.657, A:I.660, A:L.664, D:Y.631, D:L.635 6OU.10: 10 residues within 4Å: Chain B: K.504, F.507, V.508, I.573, L.574, R.575, L.577, C.578, F.582 Ligands: 6EU.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.507, B:L.574, B:L.577 6OU.11: 15 residues within 4Å: Chain B: F.649, K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain C: L.588, Y.631, S.632, C.634, L.635, F.638 Ligands: 6EU.14 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.657, B:I.660, B:L.664, C:Y.631, C:L.635 6OU.13: 15 residues within 4Å: Chain A: L.588, Y.631, S.632, C.634, L.635, F.638 Chain C: F.649, K.656, A.657, I.660, I.661, L.664, A.665, I.668 Ligands: 6EU.1 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.631, A:L.635, C:A.657, C:I.660, C:I.661 6OU.16: 10 residues within 4Å: Chain C: K.504, F.507, V.508, I.573, L.574, R.575, L.577, C.578, F.582 Ligands: 6EU.14 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.507, C:L.574, C:L.577 6OU.17: 15 residues within 4Å: Chain B: L.588, Y.631, S.632, C.634, L.635, F.638 Chain D: F.649, K.656, A.657, I.660, I.661, L.664, A.665, I.668 Ligands: 6EU.7 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:Y.631, B:L.635, D:A.657, D:I.660, D:I.661, D:L.664 6OU.20: 10 residues within 4Å: Chain D: K.504, F.507, V.508, I.573, L.574, R.575, L.577, C.578, F.582 Ligands: 6EU.18 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.507, D:L.574, D:L.577

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, D.H. et al., Vanilloid-dependent TRPV1 opening trajectory from cryoEM ensemble analysis. Nat Commun (2022)

Release Date

2022-06-01

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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