SMTL ID : 6wel.1

Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

28 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.1: 13 residues within 4Å: Chain A: D.147, L.148, P.151, E.171, C.172, Y.174, Y.197, F.200, W.204, F.207, L.359 Ligands: CPL.2, CPL.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.200, A:F.200, A:W.204, A:W.204, A:F.207, A:F.207 pi-Cation interactions: A:Y.174 CPL.2: 11 residues within 4Å: Chain A: L.137, V.317, H.321, T.356, T.358, L.359, L.360, Y.363 Chain B: N.386 Ligands: CPL.1, PX2.13 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:N.386, A:T.358 Hydrophobic interactions: A:L.137, A:V.317, A:L.359, A:Y.363, A:Y.363 CPL.4: 3 residues within 4Å: Chain A: W.329, W.333, I.387 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.329, A:W.333, A:W.333, A:W.333, A:I.387 CPL.5: 1 residues within 4Å: Chain A: W.329 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.329 CPL.6: 6 residues within 4Å: Chain A: I.140, Q.143, V.144, W.322, L.326, W.329 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.140, A:V.144, A:W.322, A:L.326, A:W.329 CPL.7: 9 residues within 4Å: Chain A: L.136, Y.287, V.290, R.291, L.294, V.311, W.314, Y.315, I.318 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.136, A:Y.287, A:R.291, A:L.294, A:V.311, A:W.314, A:W.314, A:W.314, A:I.318 CPL.8: 8 residues within 4Å: Chain A: Y.122, C.126, V.130, I.133, F.138, C.293, T.297 Ligands: CPL.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.133, A:F.138, A:T.297 CPL.11: 13 residues within 4Å: Chain B: D.147, L.148, P.151, E.171, C.172, Y.174, Y.197, F.200, W.204, F.207, L.359 Ligands: CPL.12, CPL.18 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.200, B:F.200, B:W.204, B:W.204, B:F.207, B:F.207 pi-Cation interactions: B:Y.174 CPL.12: 11 residues within 4Å: Chain B: L.137, V.317, H.321, T.356, T.358, L.359, L.360, Y.363 Chain C: N.386 Ligands: CPL.11, PX2.22 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.137, B:V.317, B:L.359, B:Y.363, B:Y.363 Hydrogen bonds: B:T.358, C:N.386 CPL.14: 3 residues within 4Å: Chain B: W.329, W.333, I.387 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.329, B:W.333, B:W.333, B:W.333, B:I.387 CPL.15: 1 residues within 4Å: Chain B: W.329 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.329 CPL.16: 6 residues within 4Å: Chain B: I.140, Q.143, V.144, W.322, L.326, W.329 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.140, B:V.144, B:W.322, B:L.326, B:W.329 CPL.17: 9 residues within 4Å: Chain B: L.136, Y.287, V.290, R.291, L.294, V.311, W.314, Y.315, I.318 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.136, B:Y.287, B:R.291, B:L.294, B:V.311, B:W.314, B:W.314, B:W.314, B:I.318 CPL.18: 8 residues within 4Å: Chain B: Y.122, C.126, V.130, I.133, F.138, C.293, T.297 Ligands: CPL.11 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.133, B:F.138, B:T.297 CPL.20: 13 residues within 4Å: Chain C: D.147, L.148, P.151, E.171, C.172, Y.174, Y.197, F.200, W.204, F.207, L.359 Ligands: CPL.21, CPL.27 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.200, C:F.200, C:W.204, C:W.204, C:F.207, C:F.207 pi-Cation interactions: C:Y.174 CPL.21: 11 residues within 4Å: Chain C: L.137, V.317, H.321, T.356, T.358, L.359, L.360, Y.363 Chain D: N.386 Ligands: CPL.20, PX2.31 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.137, C:V.317, C:L.359, C:Y.363, C:Y.363 Hydrogen bonds: C:T.358, D:N.386 CPL.23: 3 residues within 4Å: Chain C: W.329, W.333, I.387 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.329, C:W.333, C:W.333, C:W.333, C:I.387 CPL.24: 1 residues within 4Å: Chain C: W.329 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.329 CPL.25: 6 residues within 4Å: Chain C: I.140, Q.143, V.144, W.322, L.326, W.329 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.140, C:V.144, C:W.322, C:L.326, C:W.329 CPL.26: 9 residues within 4Å: Chain C: L.136, Y.287, V.290, R.291, L.294, V.311, W.314, Y.315, I.318 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.136, C:Y.287, C:R.291, C:L.294, C:V.311, C:W.314, C:W.314, C:W.314, C:I.318 CPL.27: 8 residues within 4Å: Chain C: Y.122, C.126, V.130, I.133, F.138, C.293, T.297 Ligands: CPL.20 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.133, C:F.138, C:T.297 CPL.29: 13 residues within 4Å: Chain D: D.147, L.148, P.151, E.171, C.172, Y.174, Y.197, F.200, W.204, F.207, L.359 Ligands: CPL.30, CPL.36 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.200, D:F.200, D:W.204, D:W.204, D:F.207, D:F.207 pi-Cation interactions: D:Y.174 CPL.30: 11 residues within 4Å: Chain A: N.386 Chain D: L.137, V.317, H.321, T.356, T.358, L.359, L.360, Y.363 Ligands: PX2.3, CPL.29 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.137, D:V.317, D:L.359, D:Y.363, D:Y.363 Hydrogen bonds: D:T.358, A:N.386 CPL.32: 3 residues within 4Å: Chain D: W.329, W.333, I.387 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.329, D:W.333, D:W.333, D:W.333, D:I.387 CPL.33: 1 residues within 4Å: Chain D: W.329 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.329 CPL.34: 6 residues within 4Å: Chain D: I.140, Q.143, V.144, W.322, L.326, W.329 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.140, D:V.144, D:W.322, D:L.326, D:W.329 CPL.35: 9 residues within 4Å: Chain D: L.136, Y.287, V.290, R.291, L.294, V.311, W.314, Y.315, I.318 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.136, D:Y.287, D:R.291, D:L.294, D:V.311, D:W.314, D:W.314, D:W.314, D:I.318 CPL.36: 8 residues within 4Å: Chain D: Y.122, C.126, V.130, I.133, F.138, C.293, T.297 Ligands: CPL.29 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.133, D:F.138, D:T.297

8 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX2.3: 7 residues within 4Å: Chain A: W.333, R.385, N.386, I.387, A.390 Chain D: L.360 Ligands: CPL.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.387, A:A.390 Salt bridges: A:R.385 PX2.9: 8 residues within 4Å: Chain A: R.291, Y.315, I.316, I.319, I.402, T.405, N.409 Chain D: M.413 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.316, A:I.319, A:I.402, A:T.405 Salt bridges: A:R.291 PX2.13: 7 residues within 4Å: Chain A: L.360 Chain B: W.333, R.385, N.386, I.387, A.390 Ligands: CPL.2 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.387, B:A.390 Salt bridges: B:R.385 PX2.19: 9 residues within 4Å: Chain A: M.413, I.414 Chain B: R.291, Y.315, I.316, I.319, I.402, T.405, N.409 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.316, B:I.319, B:I.402, B:T.405, A:I.414 Salt bridges: B:R.291 PX2.22: 7 residues within 4Å: Chain B: L.360 Chain C: W.333, R.385, N.386, I.387, A.390 Ligands: CPL.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.387, C:A.390 Salt bridges: C:R.385 PX2.28: 10 residues within 4Å: Chain B: M.413, I.414, M.417 Chain C: R.291, Y.315, I.316, I.319, I.402, T.405, N.409 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.316, C:I.319, C:I.402, C:T.405, B:I.414 Salt bridges: C:R.291 PX2.31: 7 residues within 4Å: Chain C: L.360 Chain D: W.333, R.385, N.386, I.387, A.390 Ligands: CPL.21 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.387, D:A.390 Salt bridges: D:R.385 PX2.37: 10 residues within 4Å: Chain C: M.413, I.414, M.417 Chain D: R.291, Y.315, I.316, I.319, I.402, T.405, N.409 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.316, D:I.319, D:I.402, D:T.405, C:I.414 Salt bridges: D:R.291

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

NA.10: 4 residues within 4Å: Chain A: E.379 Chain B: E.379 Chain C: E.379 Chain D: E.379 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Mechanism of ligand activation of a eukaryotic cyclic nucleotide-gated channel. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-06-03

Peptides

Cyclic nucleotide-gated cation channel: 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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Cyclic nucleotide-gated cation channel