9YKJ | pdb_00009ykj

Hna Dimer

  • Classification: IMMUNE SYSTEM
  • Organism(s): Sinorhizobium meliloti
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2025-10-07 Released: 2025-12-10 
  • Deposition Author(s): Hooper, M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Phage-encoded factor stimulates DNA degradation by the Hna anti-phage defense system.

Hooper, M.M.Hoover, B.T.Zhang, H.Franco, A.S.Finkelstein, I.J.Taylor, D.W.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.11.12.688083
  • Primary Citation of Related Structures:  
    9YHN, 9YKJ

  • PubMed Abstract: 

    Prokaryotic organisms have evolved unique strategies to acquire immunity against the constant threat of bacteriophage (phage) and mobile genetic elements. Hna is a broadly distributed anti-phage immune system that confers resistance against diverse phage by eliciting an abortive infection response. Using a combination of biochemistry, cryo-electron microscopy, and single-molecule fluorescence imaging, we reveal that Hna functions as a 3'-5' single-stranded DNA exonuclease that forms an auto-inhibited dimer under physiological ATP concentrations. We observed that Hna autoinhibition can be overcome by incorporation of a phage-encoded single-stranded DNA binding protein (SSB), stimulating unregulated Hna nuclease activity. Furthermore, phage escape mutants encode SSB variants that evade Hna surveillance by adopting higher order stoichiometries with enhanced DNA binding affinity. Our work establishes the molecular basis of Hna-mediated anti-phage activity and provides novel insights into how phage-encoded proteins can directly stimulate a bacterial immune response.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase ATP-binding domain-containing protein
A, B
845Sinorhizobium melilotiMutation(s): 0 
Gene Names: SMa2245
UniProt
Find proteins for Q92XN4 (Rhizobium meliloti (strain 1021))
Explore Q92XN4 
Go to UniProtKB:  Q92XN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92XN4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-12-10 
  • Deposition Author(s): Hooper, M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Welch FoundationUnited StatesF-1938

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release