8VX9

Structure of HamAB apo complex from the Escherichia coli Hachiman defense system


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Hachiman is a genome integrity sensor.

Tuck, O.T.Adler, B.A.Armbruster, E.G.Lahiri, A.Hu, J.J.Zhou, J.Pogliano, J.Doudna, J.A.

(2024) Biorxiv 

  • DOI: https://doi.org/10.1101/2024.02.29.582594
  • Primary Citation of Related Structures:  
    8VX9, 8VXA, 8VXC, 8VXY

  • PubMed Abstract: 

    Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman comprises a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact dsDNA. When the HamAB complex detects DNA damage, HamB helicase activity liberates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating 'phantom' cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and eukaryotic enzymes suggest this bacterial immune system has been repurposed for diverse functions across all domains of life.


  • Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, Berkeley, CA USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HamA259Escherichia coliMutation(s): 0 
Gene Names: HamA
UniProt
Find proteins for Q6XGE5 (Escherichia coli)
Explore Q6XGE5 
Go to UniProtKB:  Q6XGE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XGE5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HamB1,174Escherichia coliMutation(s): 0 
Gene Names: HamB
UniProt
Find proteins for A0A426EXV0 (Escherichia coli)
Explore A0A426EXV0 
Go to UniProtKB:  A0A426EXV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A426EXV0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX1.19.2-4158

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references