DdmD monomer in complex with ssDNA

Experimental Data Snapshot

  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Plasmid targeting and destruction by the DdmDE bacterial defence system.

Bravo, J.P.K.Ramos, D.A.Fregoso Ocampo, R.Ingram, C.Taylor, D.W.

(2024) Nature 630: 961-967

  • DOI: https://doi.org/10.1038/s41586-024-07515-9
  • Primary Citation of Related Structures:  
    8U0J, 8U0U, 8U0W, 8U3K, 9BQV

  • PubMed Abstract: 

    Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation 1 . Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET) 2 . Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE-guide-target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.

  • Organizational Affiliation

    Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. jack.bravo@ist.ac.at.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase/UvrB N-terminal domain-containing protein1,220Vibrio choleraeMutation(s): 0 
Gene Names: ERS013206_03454
Find proteins for B9TSM3 (Vibrio cholerae)
Explore B9TSM3 
Go to UniProtKB:  B9TSM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9TSM3
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*AP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')B [auth C]12synthetic construct
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesF-1938
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM138348

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release