SMTL ID : 8t1e.1

Closed-state cryo-EM structure of full-length human TRPV4 in the presence of 4a-PDD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

32 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: 9 residues within 4Å: Chain A: L.559, I.571, E.572, A.573, F.580, L.584, M.587 Chain B: Y.691 Ligands: 9ZR.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.559, A:F.580, A:F.580 9ZR.2: 11 residues within 4Å: Chain A: I.473, N.474, S.477, C.480, A.481, T.520, D.546, Y.553, Y.591 Ligands: 9ZR.3, 9ZR.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.481, A:T.520 Hydrogen bonds: A:N.474 Salt bridges: A:D.546 pi-Cation interactions: A:Y.591 9ZR.3: 8 residues within 4Å: Chain A: R.460, W.463, A.468, Y.472, V.476 Ligands: 9ZR.2, 9ZR.5, 9ZR.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.472, A:Y.472, A:Y.472, A:Y.472 Hydrogen bonds: A:R.460 9ZR.4: 10 residues within 4Å: Chain A: F.485, Y.502, L.511, E.514, S.563, A.564, Y.567, L.568, Y.574, M.578 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.485, A:Y.502, A:L.511, A:A.564, A:Y.567, A:L.568, A:Y.574, A:M.578 9ZR.5: 11 residues within 4Å: Chain A: L.479, Y.490, Y.491 Chain B: L.619, I.626, R.661, D.662, F.666 Ligands: 9ZR.3, 9ZR.8, YJ0.22 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.619, B:I.626, B:F.666 Salt bridges: B:D.662 Hydrogen bonds: A:Y.491, A:Y.491 9ZR.6: 9 residues within 4Å: Chain A: R.464, K.465, S.470, N.474, S.747, F.748, L.752, A.755 Ligands: 9ZR.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.752, A:A.755 Hydrogen bonds: A:N.474, A:S.747 9ZR.8: 12 residues within 4Å: Chain A: V.475, A.589, F.592, T.593, L.596, L.598 Chain B: F.611, F.615, L.619 Ligands: 9ZR.3, 9ZR.5, YJ0.22 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.611, B:F.615, B:L.619, B:L.619, A:V.475, A:L.596 9ZR.9: 12 residues within 4Å: Chain A: K.690, Y.691, P.692, V.693, V.694, I.697, T.701, I.704, L.705 Ligands: YJ0.10, 9ZR.37, YJ0.43 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.693, A:I.697, A:I.697, A:T.701, A:I.704, A:L.705, A:L.705 Hydrogen bonds: A:K.690, A:V.693, A:V.694 9ZR.14: 12 residues within 4Å: Chain B: K.690, Y.691, P.692, V.693, V.694, I.697, T.701, I.704, L.705 Ligands: 9ZR.1, YJ0.7, YJ0.15 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.693, B:I.697, B:I.697, B:T.701, B:I.704, B:L.705, B:L.705 Hydrogen bonds: B:K.690, B:V.693, B:V.694 9ZR.16: 9 residues within 4Å: Chain B: L.559, I.571, E.572, A.573, F.580, L.584, M.587 Chain C: Y.691 Ligands: 9ZR.24 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.559, B:F.580, B:F.580 9ZR.17: 11 residues within 4Å: Chain B: I.473, N.474, S.477, C.480, A.481, T.520, D.546, Y.553, Y.591 Ligands: 9ZR.18, 9ZR.21 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.481, B:T.520 Salt bridges: B:D.546 pi-Cation interactions: B:Y.591 9ZR.18: 9 residues within 4Å: Chain B: R.460, W.463, A.468, V.469, Y.472, V.476 Ligands: 9ZR.17, 9ZR.20, 9ZR.23 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.469, B:Y.472, B:Y.472, B:Y.472, B:Y.472 Hydrogen bonds: B:R.460 9ZR.19: 10 residues within 4Å: Chain B: F.485, Y.502, L.511, E.514, S.563, A.564, Y.567, L.568, Y.574, M.578 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.485, B:Y.502, B:L.511, B:A.564, B:Y.567, B:L.568, B:Y.574, B:M.578 9ZR.20: 11 residues within 4Å: Chain B: L.479, Y.490, Y.491 Chain C: L.619, I.626, R.661, D.662, F.666 Ligands: 9ZR.18, 9ZR.23, YJ0.32 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.619, C:I.626, C:F.666 Salt bridges: C:D.662 Hydrogen bonds: B:Y.491, B:Y.491 9ZR.21: 9 residues within 4Å: Chain B: R.464, K.465, S.470, N.474, S.747, F.748, L.752, A.755 Ligands: 9ZR.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.752, B:A.755 Hydrogen bonds: B:N.474, B:S.747 9ZR.23: 11 residues within 4Å: Chain B: V.475, A.589, F.592, L.596, L.598 Chain C: F.611, F.615, L.619 Ligands: 9ZR.18, 9ZR.20, YJ0.32 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:V.475, B:F.592, B:L.596, C:F.611, C:F.615, C:L.619, C:L.619 9ZR.24: 12 residues within 4Å: Chain C: K.690, Y.691, P.692, V.693, V.694, I.697, T.701, I.704, L.705 Ligands: 9ZR.16, YJ0.22, YJ0.25 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.693, C:I.697, C:I.697, C:T.701, C:I.704, C:L.705, C:L.705 Hydrogen bonds: C:K.690, C:V.693, C:V.694 9ZR.26: 9 residues within 4Å: Chain C: L.559, I.571, E.572, A.573, F.580, L.584, M.587 Chain D: Y.691 Ligands: 9ZR.35 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.559, C:F.580, C:F.580 9ZR.27: 12 residues within 4Å: Chain C: I.473, N.474, S.477, C.480, A.481, T.520, F.524, D.546, Y.553, Y.591 Ligands: 9ZR.28, 9ZR.31 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.481, C:T.520 Salt bridges: C:D.546 pi-Cation interactions: C:Y.591 9ZR.28: 9 residues within 4Å: Chain C: R.460, W.463, A.468, V.469, Y.472, V.476 Ligands: 9ZR.27, 9ZR.30, 9ZR.33 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.469, C:Y.472, C:Y.472, C:Y.472, C:Y.472 Hydrogen bonds: C:R.460 9ZR.29: 10 residues within 4Å: Chain C: F.485, Y.502, L.511, E.514, S.563, A.564, Y.567, L.568, Y.574, M.578 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.485, C:Y.502, C:L.511, C:A.564, C:Y.567, C:L.568, C:Y.574, C:M.578 9ZR.30: 11 residues within 4Å: Chain C: L.479, Y.490, Y.491 Chain D: L.619, I.626, R.661, D.662, F.666 Ligands: 9ZR.28, 9ZR.33, YJ0.43 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.619, D:I.626, D:F.666 Salt bridges: D:D.662 Hydrogen bonds: C:Y.491, C:Y.491 9ZR.31: 9 residues within 4Å: Chain C: R.464, K.465, S.470, N.474, S.747, F.748, L.752, A.755 Ligands: 9ZR.27 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.752, C:A.755 Hydrogen bonds: C:N.474, C:S.747 9ZR.33: 11 residues within 4Å: Chain C: V.475, A.589, F.592, L.596, L.598 Chain D: F.611, F.615, L.619 Ligands: 9ZR.28, 9ZR.30, YJ0.43 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.611, D:F.615, D:L.619, D:L.619, C:V.475, C:F.592, C:L.596 9ZR.34: 10 residues within 4Å: Chain A: F.615, L.619 Chain D: V.475, A.589, F.592, L.596, L.598 Ligands: YJ0.7, 9ZR.39, 9ZR.41 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.615, A:L.619, A:L.619, D:V.475, D:F.592, D:L.596 9ZR.35: 12 residues within 4Å: Chain D: K.690, Y.691, P.692, V.693, V.694, I.697, T.701, I.704, L.705 Ligands: 9ZR.26, YJ0.32, YJ0.36 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:V.693, D:I.697, D:I.697, D:T.701, D:I.704, D:L.705, D:L.705 Hydrogen bonds: D:K.690, D:V.693, D:V.694 9ZR.37: 9 residues within 4Å: Chain A: Y.691 Chain D: L.559, I.571, E.572, A.573, F.580, L.584, M.587 Ligands: 9ZR.9 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.559, D:F.580, D:F.580 9ZR.38: 11 residues within 4Å: Chain D: I.473, N.474, S.477, C.480, A.481, T.520, D.546, Y.553, Y.591 Ligands: 9ZR.39, 9ZR.42 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:A.481, D:T.520 Salt bridges: D:D.546 pi-Cation interactions: D:Y.591 9ZR.39: 9 residues within 4Å: Chain D: R.460, W.463, A.468, V.469, Y.472, V.476 Ligands: 9ZR.34, 9ZR.38, 9ZR.41 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.469, D:Y.472, D:Y.472, D:Y.472, D:Y.472 Hydrogen bonds: D:R.460 9ZR.40: 10 residues within 4Å: Chain D: F.485, Y.502, L.511, E.514, S.563, A.564, Y.567, L.568, Y.574, M.578 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.485, D:Y.502, D:L.511, D:A.564, D:Y.567, D:L.568, D:Y.574, D:M.578 9ZR.41: 11 residues within 4Å: Chain A: L.619, I.626, R.661, D.662, F.666 Chain D: L.479, Y.490, Y.491 Ligands: YJ0.7, 9ZR.34, 9ZR.39 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.619, A:I.626, A:F.666 Salt bridges: A:D.662 Hydrogen bonds: D:Y.491, D:Y.491 9ZR.42: 9 residues within 4Å: Chain D: R.464, K.465, S.470, N.474, S.747, F.748, L.752, A.755 Ligands: 9ZR.38 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.752, D:A.755 Hydrogen bonds: D:N.474, D:S.747

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)

YJ0.7: 8 residues within 4Å: Chain A: L.622, F.666, S.667, L.670 Ligands: 9ZR.14, YJ0.15, 9ZR.34, 9ZR.41 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.622, A:F.666, A:L.670 YJ0.10: 9 residues within 4Å: Chain A: P.692, V.693, I.696, V.700 Chain D: L.618, M.625, L.671 Ligands: 9ZR.9, YJ0.43 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:V.693, A:V.693, A:I.696, D:L.618, D:L.671 Hydrogen bonds: A:V.693 YJ0.15: 8 residues within 4Å: Chain A: L.618, M.625, L.671 Chain B: V.693, I.696, V.700 Ligands: YJ0.7, 9ZR.14 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.618, A:L.671, B:V.693, B:I.696 Hydrogen bonds: B:V.693 YJ0.22: 8 residues within 4Å: Chain B: L.622, F.666, S.667, L.670 Ligands: 9ZR.5, 9ZR.8, 9ZR.24, YJ0.25 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.622, B:F.666, B:L.670 YJ0.25: 8 residues within 4Å: Chain B: L.618, M.625, L.671 Chain C: V.693, I.696, V.700 Ligands: YJ0.22, 9ZR.24 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.618, B:L.671, C:V.693, C:V.693, C:I.696 Hydrogen bonds: C:V.693 YJ0.32: 8 residues within 4Å: Chain C: L.622, F.666, S.667, L.670 Ligands: 9ZR.20, 9ZR.23, 9ZR.35, YJ0.36 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.622, C:F.666, C:L.670 YJ0.36: 8 residues within 4Å: Chain C: L.618, M.625, L.671 Chain D: V.693, I.696, V.700 Ligands: YJ0.32, 9ZR.35 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.693, D:I.696, C:L.618, C:L.671 Hydrogen bonds: D:V.693 YJ0.43: 8 residues within 4Å: Chain D: L.622, F.666, S.667, L.670 Ligands: 9ZR.9, YJ0.10, 9ZR.30, 9ZR.33 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.622, D:F.666, D:L.670

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

NA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.12: 1 residues within 4Å: Ligands: NA.13 No protein-ligand interaction detected (PLIP) NA.13: 5 residues within 4Å: Chain A: D.682 Chain B: D.682 Chain C: D.682 Chain D: D.682 Ligands: NA.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A: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: 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

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