8ZGI | pdb_00008zgi

Crystal structure of DUF4297 from E.Coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.322 (Depositor), 0.332 (DCC) 
  • R-Value Work: 
    0.283 (Depositor), 0.287 (DCC) 
  • R-Value Observed: 
    0.284 (Depositor) 

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


Literature

DUF4297 and HerA form abortosome to mediate bacterial immunity against phage infection.

Tang, D.Liu, T.Chen, Y.Zhu, Z.Chen, H.Chen, Q.Yu, Y.

(2025) Mol Cell 85: 1176

  • DOI: https://doi.org/10.1016/j.molcel.2024.12.010
  • Primary Citation of Related Structures:  
    8ZGI, 8ZIQ, 8ZIR, 8ZIS, 8ZIT

  • PubMed Abstract: 

    Immune receptors form higher-order complexes known as inflammasomes in animals and resistosomes in plants to mediate immune signaling. Here, we report a similar bacterial protein complex, DUF4297-HerA, which induces abortive infection to mediate anti-phage immunity by coupling nuclease and ATPase activities. Therefore, we name this defense system "Hailibu" after a hunter in a popular folk tale who sacrifices himself to save his village. Cryoelectron microscopy (cryo-EM) results reveal that DUF4297 and HerA assemble into a higher-order complex, reminiscent of apoptosome, inflammasome, or resistosome, which we refer to as an abortosome. By capturing cryo-EM structures of the pre-loading, DNA-loading, and DNA-transporting states during Hailibu abortosome processing of DNA, we propose that DNA substrates are loaded through the HerA hexamer, with adenosine triphosphate (ATP) hydrolysis providing the energy to transport DNA substrates to the clustered DUF4297 Cap4 nuclease domains for degradation. This study demonstrates the existence of analogous multiprotein complexes in innate immunity across the kingdoms of life.


  • Organizational Affiliation
    • Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Restriction endonuclease
A, B
394Escherichia coliMutation(s): 0 
Gene Names: CG692_10945
UniProt
Find proteins for A0A776KMR6 (Escherichia coli)
Explore A0A776KMR6 
Go to UniProtKB:  A0A776KMR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A776KMR6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.322 (Depositor), 0.332 (DCC) 
  • R-Value Work:  0.283 (Depositor), 0.287 (DCC) 
  • R-Value Observed: 0.284 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.296α = 90
b = 144.296β = 90
c = 262.742γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references