8ZIR | pdb_00008zir

DUF4297-HerA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
DUF4297
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
397Agrobacterium tumefaciensMutation(s): 0 
UniProt
Find proteins for A0AA92H752 (Rhizobium rhizogenes)
Explore A0AA92H752 
Go to UniProtKB:  A0AA92H752
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA92H752
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HerA
M, N, O, P, Q
M, N, O, P, Q, R
617Agrobacterium tumefaciensMutation(s): 0 
UniProt
Find proteins for A0AA92H7C1 (Rhizobium rhizogenes)
Explore A0AA92H7C1 
Go to UniProtKB:  A0AA92H7C1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA92H7C1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection