SMTL ID : 7rqv.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

LBN.1: 17 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, E.513, F.516, Y.554, Y.555 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.443 Hydrogen bonds: A:Y.487, A:Y.555 Salt bridges: A:E.513 pi-Cation interactions: A:F.516 LBN.9: 17 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, E.513, F.516, Y.554, Y.555 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.443 Hydrogen bonds: B:Y.487, B:Y.555 Salt bridges: B:E.513 pi-Cation interactions: B:F.516 LBN.14: 17 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, E.513, F.516, Y.554, Y.555 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.443 Hydrogen bonds: C:Y.487, C:Y.555 Salt bridges: C:E.513 pi-Cation interactions: C:F.516 LBN.18: 17 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, E.513, F.516, Y.554, Y.555 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.443 Hydrogen bonds: D:Y.487, D:Y.555 Salt bridges: D:E.513 pi-Cation interactions: D:F.516

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

6OU.2: 17 residues within 4Å: Chain A: Y.584, L.585, L.588, L.630, Y.631, C.634, L.635, F.638 Chain C: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Ligands: 6OU.3, 6EU.5 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:Y.631, C:A.657, C:I.661, C:L.664, C:L.664 Salt bridges: C:K.656, C:K.656 6OU.3: 11 residues within 4Å: Chain A: L.585, V.586, F.589, L.630 Chain D: I.446, T.449, A.450, Y.453, Y.454, W.549 Ligands: 6OU.2 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.589, A:F.589, D:T.449, D:W.549 6OU.4: 14 residues within 4Å: Chain A: F.448, A.452, V.475, E.478, I.479, S.481, V.482, M.523, S.526, V.527, Y.530, F.531, Y.537, M.541 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.448, A:E.478, A:V.482, A:Y.530, A:Y.530 6OU.6: 11 residues within 4Å: Chain A: I.446, T.449, A.450, Y.453, Y.454, W.549 Chain C: L.585, V.586, F.589, L.630 Ligands: 6OU.15 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.589, C:F.589 6OU.10: 17 residues within 4Å: Chain B: Y.584, L.585, L.588, L.630, Y.631, C.634, L.635, F.638 Chain D: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Ligands: 6OU.11, 6EU.13 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:A.657, D:I.661, D:L.664, D:L.664, B:Y.631 Salt bridges: D:K.656, D:K.656 6OU.11: 11 residues within 4Å: Chain B: L.585, V.586, F.589, L.630 Chain C: I.446, T.449, A.450, Y.453, Y.454, W.549 Ligands: 6OU.10 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.549, B:F.589, B:F.589 6OU.12: 14 residues within 4Å: Chain B: F.448, A.452, V.475, E.478, I.479, S.481, V.482, M.523, S.526, V.527, Y.530, F.531, Y.537, M.541 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.448, B:E.478, B:V.482, B:Y.530, B:Y.530 6OU.15: 17 residues within 4Å: Chain B: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain C: Y.584, L.585, L.588, L.630, Y.631, C.634, L.635, F.638 Ligands: 6OU.6, 6EU.17 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.657, B:I.661, B:L.664, B:L.664, C:Y.631 Salt bridges: B:K.656, B:K.656 6OU.16: 14 residues within 4Å: Chain C: F.448, A.452, V.475, E.478, I.479, S.481, V.482, M.523, S.526, V.527, Y.530, F.531, Y.537, M.541 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.448, C:E.478, C:V.482, C:Y.530, C:Y.530 6OU.19: 17 residues within 4Å: Chain A: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain D: Y.584, L.585, L.588, L.630, Y.631, C.634, L.635, F.638 Ligands: 6OU.20, 6EU.22 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:A.657, A:I.661, A:L.664, D:Y.631 Salt bridges: A:K.656, A:K.656 6OU.20: 11 residues within 4Å: Chain B: I.446, T.449, A.450, Y.453, Y.454, W.549 Chain D: L.585, V.586, F.589, L.630 Ligands: 6OU.19 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.589, D:F.589, B:W.549 6OU.21: 14 residues within 4Å: Chain D: F.448, A.452, V.475, E.478, I.479, S.481, V.482, M.523, S.526, V.527, Y.530, F.531, Y.537, M.541 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.448, D:E.478, D:V.482, D:Y.530, D:Y.530

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.5: 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, V.567, 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.2 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.511, A:L.515, A:F.543, C:I.668, C:L.669, C:L.669 Hydrogen bonds: A:Y.511, A:T.550, A:R.557 pi-Stacking: A:Y.511 6EU.13: 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, V.567, 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.10 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:I.668, D:L.669, D:L.669, B:Y.511, B:L.515, B:F.543 Hydrogen bonds: B:Y.511, B:T.550, B:R.557 pi-Stacking: B:Y.511 6EU.17: 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, V.567, I.569, E.570, I.573, L.574, L.577 Ligands: 6OU.15 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.511, C:L.515, C:F.543, B:I.668, B:L.669, B:L.669 Hydrogen bonds: C:Y.511, C:T.550, C:R.557 pi-Stacking: C:Y.511 6EU.22: 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, V.567, I.569, E.570, I.573, L.574, L.577 Ligands: 6OU.19 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.511, D:L.515, D:F.543, A:I.668, A:L.669, A:L.669 Hydrogen bonds: D:Y.511, D:T.550, D:R.557 pi-Stacking: D:Y.511

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

NA.7: 4 residues within 4Å: Chain A: G.643 Chain B: G.643 Chain C: G.643 Chain D: G.643 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.643 NA.8: 2 residues within 4Å: Chain C: Y.671 Chain D: Y.671 No protein-ligand interaction detected (PLIP)

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
C

C
D

D
B

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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