SMTL ID : 8t1b.1

Cryo-EM structure of full-length human TRPV4 in apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

40 x 9ZR: [(2~{R})-2-[(~{Z})-hexadec-9-enoyl]oxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (~{Z})-docos-13-enoate(Non-covalent)

9ZR.1: 15 residues within 4Å: Chain A: I.555, V.558, I.571, E.572, A.573, A.576, V.577, F.580, V.583, L.584, M.587 Chain B: Y.691 Ligands: 9ZR.2, 9ZR.9, 9ZR.18 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.555, A:V.558, A:A.576, A:F.580, A:F.580, A:F.580, A:V.583 Hydrogen bonds: B:Y.691 9ZR.2: 5 residues within 4Å: Chain A: N.541, L.551 Ligands: 9ZR.1, 9ZR.7, 9ZR.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.551 9ZR.3: 12 residues within 4Å: Chain A: N.474, S.477, C.480, A.481, I.516, T.520, F.524, D.546, Y.553, Y.591 Ligands: 9ZR.4, 9ZR.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.481, A:I.516, A:T.520 Salt bridges: A:D.546 pi-Cation interactions: A:Y.553 9ZR.4: 8 residues within 4Å: Chain A: W.463, R.464, A.468, Y.472, V.476 Ligands: 9ZR.3, 9ZR.6, 9ZR.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.472, A:Y.472, A:Y.472, A:V.476 9ZR.5: 9 residues within 4Å: Chain A: F.485, L.511, E.514, T.517, S.563, A.564, Y.567, L.568, M.578 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.485, A:E.514, A:T.517, A:A.564, A:L.568 9ZR.6: 14 residues within 4Å: Chain A: V.476, L.479, T.486, Y.490, Y.491 Chain B: L.623, I.626, P.638, R.661, S.663, F.666 Ligands: 9ZR.4, 9ZR.25, YJ0.28 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.623, B:I.626, B:F.666, A:V.476, A:L.479, A:L.479, A:T.486 Hydrogen bonds: B:S.663 9ZR.7: 13 residues within 4Å: Chain A: K.612, F.615, L.619 Chain D: V.475, A.589, F.592, L.596, K.597, L.598 Ligands: 9ZR.2, YJ0.10, 9ZR.46, 9ZR.48 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:V.475, D:L.596, D:L.596, D:L.598, A:F.615, A:L.619 9ZR.8: 9 residues within 4Å: Chain A: K.465, V.469, S.470, N.474, D.743, S.747, F.748, F.756 Ligands: 9ZR.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.469, A:F.756 Hydrogen bonds: A:N.474 9ZR.9: 8 residues within 4Å: Chain A: F.525, F.554, I.561, A.565, L.566, A.569, I.571 Ligands: 9ZR.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.554, A:F.554, A:I.561 9ZR.11: 15 residues within 4Å: Chain A: K.690, Y.691 Chain D: V.558, I.571, E.572, A.573, A.576, V.577, F.580, V.583, L.584, M.587 Ligands: 9ZR.12, 9ZR.44, 9ZR.51 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:Y.691 Salt bridges: A:K.690 Hydrophobic interactions: D:V.558, D:F.580, D:F.580, D:V.583 9ZR.12: 10 residues within 4Å: Chain A: V.693, V.694, T.701, I.704, L.705 Chain D: F.580 Ligands: 9ZR.11, YJ0.13, 9ZR.44, YJ0.52 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:F.580, A:V.693, A:T.701, A:I.704, A:L.705 Hydrogen bonds: A:V.694 9ZR.18: 7 residues within 4Å: Chain A: F.580 Chain B: V.693, I.704 Ligands: 9ZR.1, 9ZR.2, YJ0.10, YJ0.19 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.580, B:V.693, B:I.704 9ZR.20: 4 residues within 4Å: Chain B: N.541 Ligands: 9ZR.25, 9ZR.29, 9ZR.30 No protein-ligand interaction detected (PLIP) 9ZR.21: 12 residues within 4Å: Chain B: N.474, S.477, C.480, A.481, I.516, T.520, F.524, D.546, Y.553, Y.591 Ligands: 9ZR.22, 9ZR.26 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.481, B:I.516, B:T.520 Salt bridges: B:D.546 pi-Cation interactions: B:Y.553 9ZR.22: 9 residues within 4Å: Chain B: W.463, R.464, A.468, Y.472, V.475, V.476 Ligands: 9ZR.21, 9ZR.24, 9ZR.37 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.472, B:Y.472, B:Y.472, B:Y.472, B:V.475, B:V.476 9ZR.23: 9 residues within 4Å: Chain B: F.485, L.511, E.514, T.517, S.563, A.564, Y.567, L.568, M.578 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.485, B:E.514, B:T.517, B:A.564, B:L.568 9ZR.24: 12 residues within 4Å: Chain B: V.476, L.479, T.486, Y.490, Y.491 Chain C: L.623, I.626, S.663, F.666 Ligands: 9ZR.22, 9ZR.37, YJ0.40 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.623, C:I.626, C:F.666, B:V.476, B:L.479, B:L.479, B:T.486 Hydrogen bonds: C:S.663 9ZR.25: 12 residues within 4Å: Chain A: V.475, F.592, L.596, K.597, L.598 Chain B: K.612, F.615, L.619 Ligands: 9ZR.4, 9ZR.6, 9ZR.20, YJ0.28 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.615, B:L.619, A:V.475, A:L.596, A:L.598 9ZR.26: 9 residues within 4Å: Chain B: K.465, V.469, S.470, N.474, D.743, S.747, F.748, F.756 Ligands: 9ZR.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.469, B:F.756 Hydrogen bonds: B:N.474 9ZR.27: 8 residues within 4Å: Chain B: F.525, F.554, I.561, A.565, L.566, A.569, I.571 Ligands: 9ZR.29 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.554, B:F.554, B:I.561 9ZR.29: 15 residues within 4Å: Chain B: V.558, I.571, E.572, A.573, A.576, V.577, F.580, V.583, L.584, M.587 Chain C: K.690, Y.691 Ligands: 9ZR.20, 9ZR.27, 9ZR.30 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:V.558, B:F.580, B:F.580, B:F.580, B:V.583 Hydrogen bonds: C:Y.691 Salt bridges: C:K.690 9ZR.30: 9 residues within 4Å: Chain B: F.580 Chain C: V.693, V.694, T.701, I.704 Ligands: 9ZR.20, YJ0.28, 9ZR.29, YJ0.31 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.693, C:T.701, C:I.704, B:F.580 Hydrogen bonds: C:V.694 9ZR.32: 4 residues within 4Å: Chain C: N.541 Ligands: 9ZR.37, 9ZR.41, 9ZR.42 No protein-ligand interaction detected (PLIP) 9ZR.33: 12 residues within 4Å: Chain C: N.474, S.477, C.480, A.481, I.516, T.520, F.524, D.546, Y.553, Y.591 Ligands: 9ZR.34, 9ZR.38 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.481, C:I.516, C:T.520 Salt bridges: C:D.546 pi-Cation interactions: C:Y.553 9ZR.34: 9 residues within 4Å: Chain C: W.463, R.464, A.468, Y.472, V.475, V.476 Ligands: 9ZR.33, 9ZR.36, 9ZR.49 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.472, C:Y.472, C:Y.472, C:Y.472, C:V.475, C:V.476 9ZR.35: 9 residues within 4Å: Chain C: F.485, L.511, E.514, T.517, S.563, A.564, Y.567, L.568, M.578 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.485, C:E.514, C:T.517, C:A.564, C:L.568 9ZR.36: 12 residues within 4Å: Chain C: V.476, L.479, T.486, Y.490, Y.491 Chain D: L.623, I.626, S.663, F.666 Ligands: 9ZR.34, 9ZR.49, YJ0.52 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.623, D:I.626, D:F.666, C:V.476, C:L.479, C:L.479, C:T.486 Hydrogen bonds: D:S.663 9ZR.37: 12 residues within 4Å: Chain B: V.475, A.589, F.592, L.596, K.597, L.598 Chain C: K.612, F.615 Ligands: 9ZR.22, 9ZR.24, 9ZR.32, YJ0.40 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.615, B:V.475, B:L.596, B:L.596, B:L.598 9ZR.38: 9 residues within 4Å: Chain C: K.465, V.469, S.470, N.474, D.743, S.747, F.748, F.756 Ligands: 9ZR.33 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.469, C:F.756 Hydrogen bonds: C:N.474 9ZR.39: 8 residues within 4Å: Chain C: F.525, F.554, I.561, A.565, L.566, A.569, I.571 Ligands: 9ZR.41 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.554, C:F.554, C:I.561 9ZR.41: 15 residues within 4Å: Chain C: V.558, I.571, E.572, A.573, A.576, V.577, F.580, V.583, L.584, M.587 Chain D: K.690, Y.691 Ligands: 9ZR.32, 9ZR.39, 9ZR.42 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.558, C:F.580, C:F.580, C:V.583 Hydrogen bonds: D:Y.691 Salt bridges: D:K.690 9ZR.42: 9 residues within 4Å: Chain C: F.580 Chain D: V.693, V.694, T.701, I.704 Ligands: 9ZR.32, YJ0.40, 9ZR.41, YJ0.43 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.693, D:T.701, D:I.704, C:F.580 Hydrogen bonds: D:V.694 9ZR.44: 4 residues within 4Å: Chain D: N.541 Ligands: 9ZR.11, 9ZR.12, 9ZR.49 No protein-ligand interaction detected (PLIP) 9ZR.45: 12 residues within 4Å: Chain D: N.474, S.477, C.480, A.481, I.516, T.520, F.524, D.546, Y.553, Y.591 Ligands: 9ZR.46, 9ZR.50 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.481, D:I.516, D:T.520 Salt bridges: D:D.546 pi-Cation interactions: D:Y.553 9ZR.46: 10 residues within 4Å: Chain D: W.463, R.464, A.468, Y.472, V.475, V.476, S.477 Ligands: 9ZR.7, 9ZR.45, 9ZR.48 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.472, D:Y.472, D:Y.472, D:Y.472, D:V.475, D:V.476 9ZR.47: 10 residues within 4Å: Chain D: F.485, L.511, E.514, T.517, V.560, S.563, A.564, Y.567, L.568, M.578 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.485, D:E.514, D:T.517, D:A.564, D:L.568 9ZR.48: 13 residues within 4Å: Chain A: L.622, L.623, I.626, S.663, F.666 Chain D: V.476, L.479, T.486, Y.490, Y.491 Ligands: 9ZR.7, YJ0.10, 9ZR.46 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:V.476, D:L.479, D:L.479, D:T.486, A:L.622, A:L.623, A:I.626, A:F.666 Hydrogen bonds: D:Y.491 9ZR.49: 12 residues within 4Å: Chain C: V.475, A.589, F.592, L.596, K.597, L.598 Chain D: K.612, F.615 Ligands: 9ZR.34, 9ZR.36, 9ZR.44, YJ0.52 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.615, C:V.475, C:L.596, C:L.598 9ZR.50: 9 residues within 4Å: Chain D: K.465, V.469, S.470, N.474, D.743, S.747, F.748, F.756 Ligands: 9ZR.45 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.469, D:F.756 Hydrogen bonds: D:N.474 9ZR.51: 8 residues within 4Å: Chain D: F.525, F.554, I.561, A.565, L.566, A.569, I.571 Ligands: 9ZR.11 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.554, D:F.554, D:I.561

8 x YJ0: (2R)-2-{[(4-O-hexopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-4-{[(25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside(Non-covalent)

YJ0.10: 8 residues within 4Å: Chain A: L.622, F.666, S.667, L.670 Ligands: 9ZR.7, 9ZR.18, YJ0.19, 9ZR.48 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.666, A:L.670 YJ0.13: 18 residues within 4Å: Chain A: L.683, E.684, M.685, L.686, S.687, P.692, V.693, I.696, V.700 Chain D: L.618, L.622, M.625, S.667, T.668, L.671, K.675 Ligands: 9ZR.12, YJ0.52 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:I.696, A:V.700, D:L.618, D:L.622, D:L.671, D:L.671 Hydrogen bonds: A:E.684, A:M.685, D:K.675 YJ0.19: 16 residues within 4Å: Chain A: L.618, L.622, T.668, L.671, K.675 Chain B: L.683, E.684, M.685, L.686, S.687, P.692, V.693, I.696, V.700 Ligands: YJ0.10, 9ZR.18 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.618, A:L.622, A:L.671 Hydrogen bonds: A:K.675, B:E.684, B:M.685 YJ0.28: 8 residues within 4Å: Chain B: L.622, F.666, S.667, L.670 Ligands: 9ZR.6, 9ZR.25, 9ZR.30, YJ0.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.666, B:L.670 YJ0.31: 17 residues within 4Å: Chain B: L.618, L.622, M.625, S.667, T.668, L.671, K.675 Chain C: E.684, M.685, L.686, S.687, P.692, V.693, I.696, V.700 Ligands: YJ0.28, 9ZR.30 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:E.684, C:M.685, B:K.675 Hydrophobic interactions: B:L.618, B:L.622, B:L.671, B:L.671 YJ0.40: 8 residues within 4Å: Chain C: L.622, F.666, S.667, L.670 Ligands: 9ZR.24, 9ZR.37, 9ZR.42, YJ0.43 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.666, C:L.670 YJ0.43: 17 residues within 4Å: Chain C: L.618, L.622, M.625, S.667, T.668, L.671, K.675 Chain D: E.684, M.685, L.686, S.687, P.692, V.693, I.696, V.700 Ligands: YJ0.40, 9ZR.42 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.618, C:L.622, C:L.671, C:L.671 Hydrogen bonds: C:K.675, D:E.684, D:M.685 YJ0.52: 8 residues within 4Å: Chain D: L.622, F.666, S.667, L.670 Ligands: 9ZR.12, YJ0.13, 9ZR.36, 9ZR.49 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.666, D:L.670

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

NA.14: 1 residues within 4Å: Ligands: NA.15 No protein-ligand interaction detected (PLIP) NA.15: 5 residues within 4Å: Chain A: G.679 Chain B: G.679 Chain C: G.679 Chain D: G.679 Ligands: NA.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.679 NA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.17: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:D.682, C:D.682

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nadezhdin, K.D. et al., Structure of human TRPV4 in complex with GTPase RhoA. Nat Commun (2023)

Release Date

2023-07-05

Peptides

Transient receptor potential cation channel subfamily V member 4/Enhanced green fluorescent protein chimera: 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 4/Enhanced green fluorescent protein chimera

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