9JG3 | pdb_00009jg3

Structure of Cas12p-TrxA-guide RNA-target DNA complex(33-bp dsDNA)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Phage-associated Cas12p nucleases require binding to bacterial thioredoxin for activation and cleavage of target DNA.

Wang, Z.Wang, Y.Gao, H.Dai, J.Tang, N.Wang, Y.Ji, Q.

(2026) Nat Microbiol 11: 81-93

  • DOI: https://doi.org/10.1038/s41564-025-02224-z
  • Primary Citation of Related Structures:  
    9JFS, 9JG3

  • PubMed Abstract: 

    The evolutionary competition within phage-host systems led to the emergence of CRISPR-Cas defence mechanisms in bacteria and anti-CRISPR elements in bacteriophages. Although anti-CRISPR elements are well characterized, the role of bacterial factors that influence CRISPR-Cas efficacy has been comparatively overlooked. Type V CRISPR-Cas12 systems display striking functional and mechanistic diversity for nucleic acid targeting. Here we use a bioinformatic approach to identify Cas12p, a phage-associated nuclease that forms complexes with the bacterial thioredoxin protein TrxA to enable target DNA degradation. This represents an unexpected phage-bacteria interaction, in which the bacteriophage co-opts a bacterial factor to augment its own genome degradation machinery, potentially against competing phages. Biochemical characterization, cryo-EM-based structural analysis of the Cas12p-TrxA-sgRNA-dsDNA complex at 2.67 Å and bacterial defence assays reveal that TrxA directly binds and activates Cas12p, enabling its nuclease activity and subsequent CRISPR immunity. These findings expand our understanding of the multilayered intricacies of phage-bacteria molecular interactions.


  • Organizational Affiliation
    • School of Physical Science and Technology and State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cas12p741unidentifiedMutation(s): 0 
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12306
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin109Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12))
Explore P0AA25 
Go to UniProtKB:  P0AA25
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UniProt GroupP0AA25
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (246-MER)246unidentified
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (33-MER)33synthetic construct
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (33-MER)33synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22277078

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references