SMTL ID : 7rqy.1

Cryo-EM structure of the full-length TRPV1 with RTx at 25 degrees Celsius, in an open state, class B

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.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, L.673 Ligands: 6OU.3, 6OU.10 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:L.515, A:L.515, A:F.543, A:A.546, A:L.553, A:A.566, A:I.573, A:L.577, C:F.591, C:F.591, C:L.662, C:A.665, C:L.669, C:L.669, C:L.669 pi-Stacking: A:Y.511 6EU.5: 30 residues within 4Å: Chain B: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, 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, L.673 Ligands: 6OU.7, 6OU.8 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:L.515, B:L.515, B:F.543, B:A.546, B:L.553, B:A.566, B:I.573, B:L.577, D:F.591, D:F.591, D:L.662, D:A.665, D:L.669, D:L.669, D:L.669 pi-Stacking: B:Y.511 6EU.11: 30 residues within 4Å: Chain B: F.587, F.591, L.662, A.665, I.668, L.669, L.673 Chain C: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, 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.9, 6OU.13 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:F.591, B:L.662, B:A.665, B:L.669, B:L.669, B:L.669, C:L.515, C:L.515, C:F.543, C:A.546, C:L.553, C:A.566, C:I.573, C:L.577 pi-Stacking: C:Y.511 6EU.14: 30 residues within 4Å: Chain A: F.587, F.591, L.662, A.665, I.668, L.669, L.673 Chain D: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, 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.4, 6OU.16 15 PLIP interactions: 9 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:L.515, D:L.515, D:F.543, D:A.546, D:L.553, D:A.566, D:I.573, D:L.577, A:F.591, A:F.591, A:A.665, A:L.669, A:L.669, A:L.669 pi-Stacking: D:Y.511

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

LBN.2: 18 residues within 4Å: Chain A: F.436, N.437, V.440, Y.441, L.443, 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.480 Hydrogen bonds: A:Y.555 Salt bridges: A:R.491, A:E.513 pi-Cation interactions: A:F.516 LBN.6: 18 residues within 4Å: Chain B: F.436, N.437, V.440, Y.441, L.443, 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 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.480 Hydrogen bonds: B:Y.555 Salt bridges: B:R.491, B:E.513 pi-Cation interactions: B:F.516 LBN.12: 18 residues within 4Å: Chain C: F.436, N.437, V.440, Y.441, L.443, 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 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.480 Hydrogen bonds: C:Y.555 Salt bridges: C:R.491, C:E.513 pi-Cation interactions: C:F.516 LBN.15: 18 residues within 4Å: Chain D: F.436, N.437, V.440, Y.441, L.443, 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 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.480 Hydrogen bonds: D:Y.555 Salt bridges: D:R.491, D:E.513 pi-Cation interactions: D:F.516

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

6OU.3: 11 residues within 4Å: Chain A: K.504, F.507, V.508, I.573, L.574, L.577, C.578, R.579, M.581, F.582 Ligands: 6EU.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.508 6OU.4: 16 residues within 4Å: Chain A: F.649, K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain D: Y.584, L.585, L.588, Y.631, C.634, L.635, F.638 Ligands: 6EU.14 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.660, A:I.661, A:I.668, D:L.588, D:L.635 6OU.7: 16 residues within 4Å: Chain B: Y.584, L.585, L.588, Y.631, 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.5 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:I.660, D:I.661, D:I.668, B:L.588, B:L.635 6OU.8: 11 residues within 4Å: Chain B: K.504, F.507, V.508, I.573, L.574, L.577, C.578, R.579, M.581, F.582 Ligands: 6EU.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.508 6OU.9: 16 residues within 4Å: Chain B: F.649, K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain C: Y.584, L.585, L.588, Y.631, C.634, L.635, F.638 Ligands: 6EU.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.661, B:I.668, C:L.588, C:L.635 6OU.10: 16 residues within 4Å: Chain A: Y.584, L.585, L.588, Y.631, 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:L.588, A:L.635, C:I.660, C:I.661, C:I.668 6OU.13: 11 residues within 4Å: Chain C: K.504, F.507, V.508, I.573, L.574, L.577, C.578, R.579, M.581, F.582 Ligands: 6EU.11 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.508 6OU.16: 11 residues within 4Å: Chain D: K.504, F.507, V.508, I.573, L.574, L.577, C.578, R.579, M.581, F.582 Ligands: 6EU.14 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.508

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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