SMTL ID : 7lp9.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.63 Å

Oligo State

homo-tetramer

Ligands

4 x T7X: Phosphatidylinositol(Non-covalent)

T7X.1: 14 residues within 4Å: Chain A: R.409, D.509, Y.511, S.512, L.515, N.551, L.553, Y.554, R.557, E.570, K.571, I.696, Q.700 Ligands: 6OU.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.511, A:L.515, A:L.553, A:L.553, A:E.570 Hydrogen bonds: A:R.409, A:R.409, A:Y.511, A:S.512, A:K.571, A:Q.700 Salt bridges: A:R.557 T7X.16: 14 residues within 4Å: Chain B: R.409, D.509, Y.511, S.512, L.515, N.551, L.553, Y.554, R.557, E.570, K.571, I.696, Q.700 Ligands: 6OU.20 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.511, B:L.515, B:L.553, B:L.553, B:E.570 Hydrogen bonds: B:R.409, B:R.409, B:Y.511, B:S.512, B:S.512, B:K.571, B:Q.700 Salt bridges: B:R.557 T7X.27: 14 residues within 4Å: Chain C: R.409, D.509, Y.511, S.512, L.515, N.551, L.553, Y.554, R.557, E.570, K.571, I.696, Q.700 Ligands: 6OU.32 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.511, C:L.515, C:L.553, C:L.553, C:E.570 Hydrogen bonds: C:R.409, C:R.409, C:Y.511, C:S.512, C:K.571, C:Q.700 Salt bridges: C:R.557 T7X.39: 14 residues within 4Å: Chain D: R.409, D.509, Y.511, S.512, L.515, N.551, L.553, Y.554, R.557, E.570, K.571, I.696, Q.700 Ligands: 6OU.44 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.511, D:L.515, D:L.553, D:L.553, D:E.570 Hydrogen bonds: D:R.409, D:R.409, D:Y.511, D:S.512, D:K.571, D:Q.700 Salt bridges: D:R.557

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

LBN.2: 11 residues within 4Å: Chain A: N.437, V.440, L.443, Y.444, Y.487, F.488, R.491, E.513, F.516, Y.554, Y.555 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.443, A:Y.444 Hydrogen bonds: A:Y.487, A:Y.555 Salt bridges: A:R.491, A:E.513 pi-Cation interactions: A:F.516, A:Y.554 LBN.10: 10 residues within 4Å: Chain A: I.446, I.447, A.450, Y.453, Y.454, G.470, F.473, R.474 Chain D: N.628 Ligands: 6OU.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.446, A:I.447, A:A.450, A:Y.454, A:F.473 LBN.14: 10 residues within 4Å: Chain A: N.628 Chain B: I.446, I.447, A.450, Y.453, Y.454, G.470, F.473, R.474 Ligands: 6OU.13 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.446, B:I.447, B:A.450, B:Y.454, B:F.473 LBN.17: 11 residues within 4Å: Chain B: N.437, V.440, L.443, Y.444, Y.487, F.488, R.491, E.513, F.516, Y.554, Y.555 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.443, B:Y.444 Hydrogen bonds: B:Y.487, B:Y.555 Salt bridges: B:R.491, B:E.513 pi-Cation interactions: B:F.516, B:Y.554 LBN.25: 10 residues within 4Å: Chain B: N.628 Chain C: I.446, I.447, A.450, Y.453, Y.454, G.470, F.473, R.474 Ligands: 6OU.24 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.446, C:I.447, C:A.450, C:Y.454, C:F.473 LBN.28: 11 residues within 4Å: Chain C: N.437, V.440, L.443, Y.444, Y.487, F.488, R.491, E.513, F.516, Y.554, Y.555 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.443, C:Y.444 Hydrogen bonds: C:Y.487, C:Y.555 Salt bridges: C:R.491, C:E.513 pi-Cation interactions: C:F.516, C:Y.554 LBN.38: 10 residues within 4Å: Chain C: N.628 Chain D: I.446, I.447, A.450, Y.453, Y.454, G.470, F.473, R.474 Ligands: 6OU.37 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.446, D:I.447, D:A.450, D:Y.454, D:F.473 LBN.40: 11 residues within 4Å: Chain D: N.437, V.440, L.443, Y.444, Y.487, F.488, R.491, E.513, F.516, Y.554, Y.555 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.443, D:Y.444 Hydrogen bonds: D:Y.487, D:Y.555 Salt bridges: D:R.491, D:E.513 pi-Cation interactions: D:F.516, D:Y.554

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

6OU.3: 3 residues within 4Å: Chain A: V.528, L.529, R.534 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.528, A:L.529 Hydrogen bonds: A:R.534 Salt bridges: A:R.534 6OU.4: 10 residues within 4Å: Chain A: L.588, S.629, Y.631, C.634, F.638 Chain D: I.660, I.661, L.664 Ligands: 6OU.13, 6OU.36 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:I.660, D:I.661, D:L.664, A:L.588, A:Y.631, A:F.638, A:F.638 Hydrogen bonds: A:S.629 6OU.5: 7 residues within 4Å: Chain A: F.507, Y.511, L.515, L.574, C.578 Ligands: T7X.1, 6OU.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.511, A:L.515 6OU.6: 7 residues within 4Å: Chain A: C.578, R.579, F.582, L.585 Chain B: Q.561 Ligands: 6OU.5, YFP.15 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.579, A:F.582, A:L.585, B:Q.561 6OU.7: 5 residues within 4Å: Chain A: F.448, E.478, V.482, Y.530, M.541 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.448, A:V.482, A:Y.530, A:Y.530 6OU.8: 3 residues within 4Å: Chain A: F.655, V.658 Chain B: E.536 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.658 6OU.9: 6 residues within 4Å: Chain A: Y.453, Y.454 Chain D: F.589, L.630 Ligands: LBN.10, 6OU.42 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Y.453, A:Y.454 Hydrophobic interactions: D:F.589, D:F.589 6OU.13: 6 residues within 4Å: Chain A: F.589, L.630 Chain B: Y.453, Y.454 Ligands: 6OU.4, LBN.14 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.453, B:Y.454 Hydrophobic interactions: A:F.589, A:F.589 6OU.18: 3 residues within 4Å: Chain B: V.528, L.529, R.534 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.529 Hydrogen bonds: B:R.534 Salt bridges: B:R.534 6OU.19: 9 residues within 4Å: Chain A: I.660, I.661, L.664 Chain B: L.588, S.629, Y.631, C.634, F.638 Ligands: 6OU.24 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.588, B:Y.631, B:F.638, A:I.661, A:L.664 Hydrogen bonds: B:S.629 6OU.20: 7 residues within 4Å: Chain B: F.507, Y.511, L.515, L.574, C.578 Ligands: T7X.16, 6OU.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.511, B:L.515 6OU.21: 7 residues within 4Å: Chain B: C.578, R.579, F.582, L.585 Chain C: Q.561 Ligands: 6OU.20, YFP.26 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:R.579, B:F.582, B:L.585, C:Q.561 6OU.22: 5 residues within 4Å: Chain B: F.448, E.478, V.482, Y.530, M.541 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.448, B:V.482, B:Y.530, B:Y.530 6OU.23: 3 residues within 4Å: Chain B: D.654, A.657 Ligands: 6OU.30 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.657 6OU.24: 6 residues within 4Å: Chain B: F.589, L.630 Chain C: Y.453, Y.454 Ligands: 6OU.19, LBN.25 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.453, C:Y.454 Hydrophobic interactions: B:F.589, B:F.589 6OU.29: 3 residues within 4Å: Chain C: V.528, L.529, R.534 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.529 Hydrogen bonds: C:R.534 Salt bridges: C:R.534 6OU.30: 9 residues within 4Å: Chain B: I.660, I.661, L.664 Chain C: L.588, S.629, Y.631, C.634 Ligands: 6OU.23, 6OU.37 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.588, C:Y.631, B:I.661, B:L.664 Hydrogen bonds: C:S.629 6OU.32: 7 residues within 4Å: Chain C: F.507, Y.511, L.515, L.574, C.578 Ligands: T7X.27, 6OU.33 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.511, C:L.515 6OU.33: 7 residues within 4Å: Chain C: C.578, R.579, F.582, L.585 Chain D: Q.561 Ligands: YFP.31, 6OU.32 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Q.561, C:R.579, C:F.582, C:L.585 6OU.34: 5 residues within 4Å: Chain C: F.448, E.478, V.482, Y.530, M.541 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.448, C:V.482, C:Y.530, C:Y.530 6OU.35: 2 residues within 4Å: Chain C: D.654, I.661 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.661 Hydrogen bonds: C:D.654 6OU.36: 5 residues within 4Å: Chain A: E.536, F.543 Chain D: D.654, F.655 Ligands: 6OU.4 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.654 Hydrophobic interactions: A:F.543 6OU.37: 6 residues within 4Å: Chain C: F.589, L.630 Chain D: Y.453, Y.454 Ligands: 6OU.30, LBN.38 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.453, D:Y.454 Hydrophobic interactions: C:F.589, C:F.589, C:F.589 6OU.41: 3 residues within 4Å: Chain D: V.528, L.529, R.534 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.528, D:L.529 Hydrogen bonds: D:R.534 Salt bridges: D:R.534 6OU.42: 9 residues within 4Å: Chain C: I.660, I.661, L.664 Chain D: L.588, S.629, Y.631, C.634, F.638 Ligands: 6OU.9 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.588, D:Y.631, D:F.638, D:F.638, C:I.660, C:I.661, C:L.664 Hydrogen bonds: D:S.629 6OU.44: 7 residues within 4Å: Chain D: F.507, Y.511, L.515, L.574, C.578 Ligands: T7X.39, 6OU.45 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.511, D:L.515 6OU.45: 7 residues within 4Å: Chain A: Q.561 Chain D: C.578, R.579, F.582, L.585 Ligands: YFP.43, 6OU.44 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:R.579, D:F.582, D:L.585, A:Q.561 6OU.46: 5 residues within 4Å: Chain D: F.448, E.478, V.482, Y.530, M.541 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.448, D:V.482, D:Y.530, D:Y.530

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

NA.11: 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 D Hydrogen bonds: D:G.643 NA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

YFP.15: 5 residues within 4Å: Chain A: F.582 Chain B: F.559, Q.560, M.562 Ligands: 6OU.6 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.582, B:F.559, B:F.559, B:F.559 Hydrogen bonds: B:Q.560 YFP.26: 7 residues within 4Å: Chain B: F.582 Chain C: Y.435, F.438, T.556, F.559, Q.560 Ligands: 6OU.21 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.435, C:F.438, C:T.556, C:F.559, C:F.559 Hydrogen bonds: C:Q.560 YFP.31: 8 residues within 4Å: Chain C: F.582 Chain D: Y.435, F.438, T.556, F.559, Q.560, M.562 Ligands: 6OU.33 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.435, D:F.438, D:T.556, D:F.559, C:F.582 Hydrogen bonds: D:Q.560 YFP.43: 8 residues within 4Å: Chain A: Y.435, F.438, T.556, F.559, Q.560, M.562 Chain D: F.582 Ligands: 6OU.45 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.435, A:F.438, A:F.438, A:T.556, A:F.559, A:F.559, A:F.559, D:F.582 Hydrogen bonds: A:Q.560

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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