9IJM | pdb_00009ijm

Bacterial flagellar sodium-driven stator PomA5PomB2 with 100 mM NaCl and 0.1 mM phenamil


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural insight into sodium ion pathway in the bacterial flagellar stator from marine Vibrio.

Nishikino, T.Takekawa, N.Kishikawa, J.I.Hirose, M.Kojima, S.Homma, M.Kato, T.Imada, K.

(2025) Proc Natl Acad Sci U S A 122: e2415713122-e2415713122

  • DOI: https://doi.org/10.1073/pnas.2415713122
  • Primary Citation of Related Structures:  
    8ZYV, 8ZYW, 8ZYZ, 8ZZ0, 9IJM

  • PubMed Abstract: 

    Many bacteria swim in liquid or swarm on surface using the flagellum rotated by a motor driven by specific ion flow. The motor consists of the rotor and stator, and the stator converts the energy of ion flow to mechanical rotation. However, the ion pathway and the mechanism of stator rotation coupled with specific ion flow are still obscure. Here, we determined the structures of the sodium-driven stator of Vibrio , namely PomAB, in the presence and absence of sodium ions and the structure with its specific inhibitor, phenamil, by cryo-electron microscopy. The structures and following functional analysis revealed the sodium ion pathway, the mechanism of ion selectivity, and the inhibition mechanism by phenamil. We propose a model of sodium ion flow coupled with the stator rotation based on the structures. This work provides insights into the molecular mechanisms of ion specificity and conversion of the electrochemical potential into mechanical functions.


  • Organizational Affiliation
    • Division of Protein Structural Biology, Institute for Protein Research, Osaka University, Suita 565-0871, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PomB
A, B
321Vibrio alginolyticusMutation(s): 0 
Gene Names: pomB
UniProt
Find proteins for O06874 (Vibrio alginolyticus)
Explore O06874 
Go to UniProtKB:  O06874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06874
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chemotaxis protein PomA
C, D, E, F, G
253Vibrio alginolyticusMutation(s): 0 
Gene Names: pomA
UniProt
Find proteins for O06873 (Vibrio alginolyticus)
Explore O06873 
Go to UniProtKB:  O06873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06873
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP20J00329
Japan Society for the Promotion of Science (JSPS)JapanJP23K14157

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references