8H9Y image
Deposition Date 2022-10-25
Release Date 2023-07-26
Last Version Date 2024-05-29
Entry Detail
PDB ID:
8H9Y
Title:
Crystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in calcium ion condition
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.40 Å
R-Value Free:
0.26
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
I 4 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Ion transport protein
Gene (Uniprot):Abu_1752
Mutations:N49K, L176Q
Chain IDs:A
Chain Length:271
Number of Molecules:1
Biological Source:Aliarcobacter butzleri
Primary Citation
The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel.
Nat Commun 14 4236 4236 (2023)
PMID: 37454189 DOI: 10.1038/s41467-023-39987-0

Abstact

Divalent cation block is observed in various tetrameric ion channels. For blocking, a divalent cation is thought to bind in the ion pathway of the channel, but such block has not yet been directly observed. So, the behaviour of these blocking divalent cations remains still uncertain. Here, we elucidated the mechanism of the divalent cation block by reproducing the blocking effect into NavAb, a well-studied tetrameric sodium channel. Our crystal structures of NavAb mutants show that the mutations increasing the hydrophilicity of the inner vestibule of the pore domain enable a divalent cation to stack on the ion pathway. Furthermore, non-equilibrium molecular dynamics simulation showed that the stacking calcium ion repel sodium ion at the bottom of the selectivity filter. These results suggest the primary process of the divalent cation block mechanism in tetrameric cation channels.

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