SMTL ID : 7rqu.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.1: 28 residues within 4Å: Chain A: F.507, Y.511, S.512, I.514, L.515, F.516, 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.577, Q.700 Chain D: F.587, F.591, L.662, A.665, I.668, L.669 Ligands: 6OU.3, 6OU.31 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.515, A:L.515, A:L.553, D:F.591, D:L.669, D:L.669, D:L.669 Hydrogen bonds: A:Y.511, A:S.512, A:R.557 pi-Stacking: A:Y.511 6EU.12: 28 residues within 4Å: Chain B: F.507, Y.511, S.512, I.514, L.515, F.516, 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.577, Q.700 Chain C: F.587, F.591, L.662, A.665, I.668, L.669 Ligands: 6OU.14, 6OU.25 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.515, B:L.515, B:L.553, C:F.591, C:L.669, C:L.669, C:L.669 Hydrogen bonds: B:Y.511, B:S.512, B:R.557 pi-Stacking: B:Y.511 6EU.26: 28 residues within 4Å: Chain A: 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, 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.577, Q.700 Ligands: 6OU.6, 6OU.28 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.515, C:L.515, C:L.553, A:F.591, A:L.669, A:L.669, A:L.669 Hydrogen bonds: C:Y.511, C:S.512, C:R.557 pi-Stacking: C:Y.511 6EU.35: 28 residues within 4Å: Chain B: 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, 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.577, Q.700 Ligands: 6OU.20, 6OU.37 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:L.515, D:L.515, D:L.553, B:F.591, B:L.669, B:L.669, B:L.669 Hydrogen bonds: D:Y.511, D:S.512, D:R.557 pi-Stacking: D:Y.511

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

LBN.2: 17 residues within 4Å: Chain A: 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.443 Hydrogen bonds: A:Y.487, A:Y.555, A:Y.555 Salt bridges: A:R.491, A:E.513 pi-Cation interactions: A:F.516 LBN.8: 15 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 D: N.628 Ligands: 6OU.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.446, A:A.450, A:Y.454 LBN.13: 17 residues within 4Å: Chain B: 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 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.443 Hydrogen bonds: B:Y.487, B:Y.555, B:Y.555 Salt bridges: B:R.491, B:E.513 pi-Cation interactions: B:F.516 LBN.17: 15 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 C: N.628 Ligands: 6OU.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.446, B:A.450, B:Y.454 LBN.22: 15 residues within 4Å: Chain A: N.628 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 Ligands: 6OU.21 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.446, C:A.450, C:Y.454 LBN.27: 17 residues within 4Å: Chain C: 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 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.443 Hydrogen bonds: C:Y.487, C:Y.555, C:Y.555 Salt bridges: C:R.491, C:E.513 pi-Cation interactions: C:F.516 LBN.33: 15 residues within 4Å: Chain B: N.628 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 Ligands: 6OU.32 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.446, D:A.450, D:Y.454 LBN.36: 17 residues within 4Å: Chain D: 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 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.443 Hydrogen bonds: D:Y.487, D:Y.555, D:Y.555 Salt bridges: D:R.491, D:E.513 pi-Cation interactions: D:F.516

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

6OU.3: 8 residues within 4Å: Chain A: K.504, F.507, V.508, I.573, L.574, C.578 Ligands: 6EU.1, YFP.23 No protein-ligand interaction detected (PLIP) 6OU.4: 11 residues within 4Å: Chain A: F.448, A.451, A.452, E.478, I.479, S.481, V.482, V.527, Y.530, F.531, M.541 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.448, A:E.478, A:I.479, A:V.482, A:V.527, A:Y.530, A:F.531 6OU.5: 10 residues within 4Å: Chain A: D.654, F.655, K.656, A.657, V.658, I.661 Chain C: F.522, E.536, F.543 Ligands: 6OU.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.654 Hydrophobic interactions: C:F.543, C:F.543 6OU.6: 12 residues within 4Å: Chain A: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain C: S.629, Y.631 Ligands: 6OU.5, 6OU.16, 6EU.26 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.657, A:L.664, A:L.664, C:Y.631 6OU.7: 12 residues within 4Å: Chain A: I.446, T.449, A.450, Y.453, Y.454, W.549 Chain D: L.585, V.586, F.589, L.630 Ligands: LBN.8, 6OU.20 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:F.589, A:I.446 Hydrogen bonds: A:Y.454 6OU.14: 8 residues within 4Å: Chain B: K.504, F.507, V.508, I.573, L.574, C.578 Ligands: 6EU.12, YFP.34 No protein-ligand interaction detected (PLIP) 6OU.15: 11 residues within 4Å: Chain B: F.448, A.451, A.452, E.478, I.479, S.481, V.482, V.527, Y.530, F.531, M.541 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.448, B:E.478, B:I.479, B:V.482, B:V.527, B:Y.530, B:F.531 6OU.16: 12 residues within 4Å: Chain B: I.446, T.449, A.450, Y.453, Y.454, W.549 Chain C: L.585, V.586, F.589, L.630 Ligands: 6OU.6, LBN.17 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.446, C:F.589 Hydrogen bonds: B:Y.454 6OU.19: 11 residues within 4Å: Chain B: D.654, F.655, K.656, A.657, V.658, I.661 Chain D: F.522, E.536, A.539, F.543 Ligands: 6OU.20 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:A.657, D:F.543, D:F.543 Hydrogen bonds: B:D.654 6OU.20: 12 residues within 4Å: Chain B: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain D: S.629, Y.631 Ligands: 6OU.7, 6OU.19, 6EU.35 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:A.657, B:L.664, B:L.664, D:Y.631 6OU.21: 12 residues within 4Å: Chain A: L.585, V.586, F.589, L.630 Chain C: I.446, T.449, A.450, Y.453, Y.454, W.549 Ligands: LBN.22, 6OU.31 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.446, A:F.589 Hydrogen bonds: C:Y.454 6OU.24: 11 residues within 4Å: Chain B: F.522, E.536, A.539, F.543 Chain C: D.654, F.655, K.656, A.657, V.658, I.661 Ligands: 6OU.25 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.543, B:F.543, C:A.657 Hydrogen bonds: C:D.654 6OU.25: 12 residues within 4Å: Chain B: S.629, Y.631 Chain C: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Ligands: 6EU.12, 6OU.24, 6OU.32 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.657, C:L.664, C:L.664, B:Y.631 6OU.28: 8 residues within 4Å: Chain C: K.504, F.507, V.508, I.573, L.574, C.578 Ligands: YFP.18, 6EU.26 No protein-ligand interaction detected (PLIP) 6OU.29: 11 residues within 4Å: Chain C: F.448, A.451, A.452, E.478, I.479, S.481, V.482, V.527, Y.530, F.531, M.541 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.448, C:E.478, C:I.479, C:V.482, C:V.527, C:Y.530, C:F.531 6OU.30: 11 residues within 4Å: Chain A: F.522, E.536, A.539, F.543 Chain D: D.654, F.655, K.656, A.657, V.658, I.661 Ligands: 6OU.31 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.657, A:F.543, A:F.543 Hydrogen bonds: D:D.654 6OU.31: 12 residues within 4Å: Chain A: S.629, Y.631 Chain D: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Ligands: 6EU.1, 6OU.21, 6OU.30 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.657, D:L.664, D:L.664, A:Y.631 6OU.32: 12 residues within 4Å: Chain B: L.585, V.586, F.589, L.630 Chain D: I.446, T.449, A.450, Y.453, Y.454, W.549 Ligands: 6OU.25, LBN.33 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.446, B:F.589 Hydrogen bonds: D:Y.454 6OU.37: 8 residues within 4Å: Chain D: K.504, F.507, V.508, I.573, L.574, C.578 Ligands: YFP.9, 6EU.35 No protein-ligand interaction detected (PLIP) 6OU.38: 11 residues within 4Å: Chain D: F.448, A.451, A.452, E.478, I.479, S.481, V.482, V.527, Y.530, F.531, M.541 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.448, D:E.478, D:I.479, D:V.482, D:V.527, D:Y.530, D:F.531

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

YFP.9: 10 residues within 4Å: Chain A: Y.435, F.438, F.439, C.442, F.559, Q.560, Q.561, M.562 Chain D: F.582 Ligands: 6OU.37 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.435, A:F.438, A:F.559, D:F.582 YFP.18: 10 residues within 4Å: Chain B: Y.435, F.438, F.439, F.559, Q.560, Q.561, M.562, R.701 Chain C: F.582 Ligands: 6OU.28 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.435, B:F.438, B:F.559, B:F.559, C:F.582 YFP.23: 11 residues within 4Å: Chain A: F.582 Chain C: Y.435, F.438, F.439, C.442, F.559, Q.560, Q.561, M.562, R.701 Ligands: 6OU.3 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:F.582, C:Y.435, C:F.438, C:F.559, C:F.559 YFP.34: 11 residues within 4Å: Chain B: F.582 Chain D: Y.435, F.438, F.439, C.442, F.559, Q.560, Q.561, M.562, R.701 Ligands: 6OU.14 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.435, D:F.438, D:F.559, B:F.582

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

NA.10: 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 D Hydrogen bonds: D:G.643 NA.11: 4 residues within 4Å: Chain A: G.643 Chain B: G.643 Chain C: G.643 Chain D: G.643 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
B

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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