SMTL ID : 8v6k.1

Apo-state cryo-EM structure of human TRPV3 in cNW30 nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

32 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 23 residues within 4Å: Chain A: F.592, I.595, V.596, L.598, L.599, G.600, V.603, S.624, F.625, S.626, D.627, V.629 Chain D: F.449, T.456, L.457, Y.460, Y.461, W.559 Ligands: POV.3, POV.11, POV.12, POV.29, POV.30 Ligand excluded by PLIP POV.2: 24 residues within 4Å: Chain A: K.435, F.436, H.439, M.440, L.443, S.444, F.447, W.493, C.496, I.497, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, F.703, M.706, L.707, P.708, W.710, L.711, F.715 Ligand excluded by PLIP POV.3: 19 residues within 4Å: Chain A: L.513, Q.514, L.517, L.584, H.585, L.588, K.589, L.591, F.592, I.595 Chain B: I.659, I.663 Chain D: S.571, M.572 Ligands: POV.1, POV.4, POV.11, POV.12, POV.29 Ligand excluded by PLIP POV.4: 28 residues within 4Å: Chain A: L.517, S.518, W.521, F.522, I.528, L.532, L.553, A.556, L.557, A.560, N.561, L.563, V.577, I.579, Q.580, K.581, I.583, L.584, L.588 Chain B: F.597, F.601, F.656, L.657, T.660, L.664 Ligands: POV.3, POV.11, POV.12 Ligand excluded by PLIP POV.5: 21 residues within 4Å: Chain A: H.430, W.433, K.438, F.441, F.442, F.445, F.449, M.562, Y.565, T.566, G.568, F.569, Q.570, S.571, M.572, R.693, R.696 Chain B: F.592, V.596 Ligands: POV.13, POV.15 Ligand excluded by PLIP POV.6: 13 residues within 4Å: Chain A: F.449, F.450, I.453, T.454, L.457, V.458, Y.461, L.482, Q.483, G.486, W.559 Chain B: L.599 Ligands: POV.13 Ligand excluded by PLIP POV.7: 28 residues within 4Å: Chain A: I.644, Q.645, P.651, I.652, L.655, F.656, I.659, T.660, V.662, I.663, F.666, V.667 Chain D: F.590, L.591, Y.594, I.595, L.598, S.626, V.629, L.630, F.633, T.636, I.637, L.670 Ligands: POV.8, POV.33, POV.35, POV.36 Ligand excluded by PLIP POV.8: 19 residues within 4Å: Chain A: K.649, Y.650, P.651, I.652, L.653, F.656 Chain D: F.527, I.528, V.531, L.532, L.535, E.546, A.549, C.550, L.553 Ligands: POV.7, POV.33, POV.35, POV.36 Ligand excluded by PLIP POV.11: 28 residues within 4Å: Chain A: F.590, L.591, Y.594, I.595, L.598, S.626, V.629, L.630, F.633, T.636, I.637, L.670 Chain B: I.644, Q.645, P.651, I.652, L.655, F.656, I.659, T.660, V.662, I.663, F.666, V.667 Ligands: POV.1, POV.3, POV.4, POV.12 Ligand excluded by PLIP POV.12: 19 residues within 4Å: Chain A: F.527, I.528, V.531, L.532, L.535, E.546, A.549, C.550, L.553 Chain B: K.649, Y.650, P.651, I.652, L.653, F.656 Ligands: POV.1, POV.3, POV.4, POV.11 Ligand excluded by PLIP POV.13: 22 residues within 4Å: Chain A: F.449, T.456, L.457, Y.460, Y.461, W.559 Chain B: F.592, I.595, V.596, L.598, L.599, G.600, V.603, S.624, F.625, S.626, V.629 Ligands: POV.5, POV.6, POV.15, POV.21, POV.22 Ligand excluded by PLIP POV.14: 24 residues within 4Å: Chain B: K.435, F.436, H.439, M.440, L.443, S.444, F.447, W.493, C.496, I.497, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, F.703, M.706, L.707, P.708, W.710, L.711, F.715 Ligand excluded by PLIP POV.15: 19 residues within 4Å: Chain A: S.571, M.572 Chain B: L.513, Q.514, L.517, L.584, H.585, L.588, K.589, L.591, F.592, I.595 Chain C: I.659, I.663 Ligands: POV.5, POV.13, POV.16, POV.21, POV.22 Ligand excluded by PLIP POV.16: 28 residues within 4Å: Chain B: L.517, S.518, W.521, F.522, I.528, L.532, L.553, A.556, L.557, A.560, N.561, L.563, V.577, I.579, Q.580, K.581, I.583, L.584, L.588 Chain C: F.597, F.601, F.656, L.657, T.660, L.664 Ligands: POV.15, POV.21, POV.22 Ligand excluded by PLIP POV.17: 21 residues within 4Å: Chain B: H.430, W.433, K.438, F.441, F.442, F.445, F.449, M.562, Y.565, T.566, G.568, F.569, Q.570, S.571, M.572, R.693, R.696 Chain C: F.592, V.596 Ligands: POV.23, POV.25 Ligand excluded by PLIP POV.18: 14 residues within 4Å: Chain B: F.449, F.450, I.453, T.454, L.457, V.458, Y.461, L.482, Q.483, L.485, G.486, W.559 Chain C: L.599 Ligands: POV.23 Ligand excluded by PLIP POV.21: 28 residues within 4Å: Chain B: F.590, L.591, Y.594, I.595, L.598, S.626, V.629, L.630, F.633, T.636, I.637, L.670 Chain C: I.644, Q.645, P.651, I.652, L.655, F.656, I.659, T.660, V.662, I.663, F.666, V.667 Ligands: POV.13, POV.15, POV.16, POV.22 Ligand excluded by PLIP POV.22: 19 residues within 4Å: Chain B: F.527, I.528, V.531, L.532, L.535, E.546, A.549, C.550, L.553 Chain C: K.649, Y.650, P.651, I.652, L.653, F.656 Ligands: POV.13, POV.15, POV.16, POV.21 Ligand excluded by PLIP POV.23: 22 residues within 4Å: Chain B: F.449, T.456, L.457, Y.460, Y.461, W.559 Chain C: F.592, I.595, V.596, L.598, L.599, G.600, V.603, S.624, F.625, S.626, V.629 Ligands: POV.17, POV.18, POV.25, POV.31, POV.32 Ligand excluded by PLIP POV.24: 24 residues within 4Å: Chain C: K.435, F.436, H.439, M.440, L.443, S.444, F.447, W.493, C.496, I.497, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, F.703, M.706, L.707, P.708, W.710, L.711, F.715 Ligand excluded by PLIP POV.25: 19 residues within 4Å: Chain B: S.571, M.572 Chain C: L.513, Q.514, L.517, L.584, H.585, L.588, K.589, L.591, F.592, I.595 Chain D: I.659, I.663 Ligands: POV.17, POV.23, POV.26, POV.31, POV.32 Ligand excluded by PLIP POV.26: 28 residues within 4Å: Chain C: L.517, S.518, W.521, F.522, I.528, L.532, L.553, A.556, L.557, A.560, N.561, L.563, V.577, I.579, Q.580, K.581, I.583, L.584, L.588 Chain D: F.597, F.601, F.656, L.657, T.660, L.664 Ligands: POV.25, POV.31, POV.32 Ligand excluded by PLIP POV.27: 21 residues within 4Å: Chain C: H.430, W.433, K.438, F.441, F.442, F.445, F.449, M.562, Y.565, T.566, G.568, F.569, Q.570, S.571, M.572, R.693, R.696 Chain D: F.592, V.596 Ligands: POV.33, POV.35 Ligand excluded by PLIP POV.28: 14 residues within 4Å: Chain C: F.449, F.450, I.453, T.454, L.457, V.458, Y.461, L.482, Q.483, L.485, G.486, W.559 Chain D: L.599 Ligands: POV.33 Ligand excluded by PLIP POV.29: 21 residues within 4Å: Chain A: F.592, V.596 Chain D: H.430, W.433, K.438, F.441, F.442, F.445, F.449, M.562, Y.565, T.566, G.568, F.569, Q.570, S.571, M.572, R.693, R.696 Ligands: POV.1, POV.3 Ligand excluded by PLIP POV.30: 14 residues within 4Å: Chain A: L.599 Chain D: F.449, F.450, I.453, T.454, L.457, V.458, Y.461, L.482, Q.483, L.485, G.486, W.559 Ligands: POV.1 Ligand excluded by PLIP POV.31: 28 residues within 4Å: Chain C: F.590, L.591, Y.594, I.595, L.598, S.626, V.629, L.630, F.633, T.636, I.637, L.670 Chain D: I.644, Q.645, P.651, I.652, L.655, F.656, I.659, T.660, V.662, I.663, F.666, V.667 Ligands: POV.23, POV.25, POV.26, POV.32 Ligand excluded by PLIP POV.32: 19 residues within 4Å: Chain C: F.527, I.528, V.531, L.532, L.535, E.546, A.549, C.550, L.553 Chain D: K.649, Y.650, P.651, I.652, L.653, F.656 Ligands: POV.23, POV.25, POV.26, POV.31 Ligand excluded by PLIP POV.33: 22 residues within 4Å: Chain C: F.449, T.456, L.457, Y.460, Y.461, W.559 Chain D: F.592, I.595, V.596, L.598, L.599, G.600, V.603, S.624, F.625, S.626, V.629 Ligands: POV.7, POV.8, POV.27, POV.28, POV.35 Ligand excluded by PLIP POV.34: 24 residues within 4Å: Chain D: K.435, F.436, H.439, M.440, L.443, S.444, F.447, W.493, C.496, I.497, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, F.703, M.706, L.707, P.708, W.710, L.711, F.715 Ligand excluded by PLIP POV.35: 19 residues within 4Å: Chain A: I.659, I.663 Chain C: S.571, M.572 Chain D: L.513, Q.514, L.517, L.584, H.585, L.588, K.589, L.591, F.592, I.595 Ligands: POV.7, POV.8, POV.27, POV.33, POV.36 Ligand excluded by PLIP POV.36: 28 residues within 4Å: Chain A: F.597, F.601, F.656, L.657, T.660, L.664 Chain D: L.517, S.518, W.521, F.522, I.528, L.532, L.553, A.556, L.557, A.560, N.561, L.563, V.577, I.579, Q.580, K.581, I.583, L.584, L.588 Ligands: POV.7, POV.8, POV.35 Ligand excluded by PLIP

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

NA.9: 13 residues within 4Å: Chain A: G.638, L.639, G.640 Chain B: G.638, L.639, G.640 Chain C: G.638, L.639, G.640 Chain D: G.638, L.639, G.640 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.640 NA.10: 6 residues within 4Å: Chain A: G.638 Chain B: G.638 Chain C: G.638 Chain D: G.638 Ligands: NA.9, NA.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.638 NA.19: 5 residues within 4Å: Chain A: G.638 Chain B: G.638 Chain C: G.638 Chain D: G.638 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.638 NA.20: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.682, B:E.682, B:E.682, B:E.682

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nadezhdin, K.D. et al., TRPV3 activation by different agonists accompanied by lipid dissociation from the vanilloid site. Sci Adv (2024)

Release Date

2024-04-17

Peptides

Transient receptor potential cation channel subfamily V member 3: 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 3

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