8B1U

RecBCD-DNA in complex with the phage protein Abc2 and host PpiB


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub.

Wilkinson, M.Wilkinson, O.J.Feyerherm, C.Fletcher, E.E.Wigley, D.B.Dillingham, M.S.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.83409
  • Primary Citation of Related Structures:  
    8B1R, 8B1T, 8B1U

  • PubMed Abstract: 

    Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products.


  • Organizational Affiliation

    Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecBA [auth B]1,180Escherichia coliMutation(s): 1 
Gene Names: 
EC: 3.1.11.5 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for P08394 (Escherichia coli (strain K12))
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Go to UniProtKB:  P08394
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UniProt GroupP08394
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecCB [auth C]1,122Escherichia coliMutation(s): 0 
Gene Names: recCb2822JW2790
EC: 3.1.11.5
UniProt
Find proteins for P07648 (Escherichia coli (strain K12))
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Go to UniProtKB:  P07648
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UniProt GroupP07648
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecDC [auth D]608Escherichia coliMutation(s): 0 
Gene Names: recDhopEb2819JW2787
EC: 3.1.11.5 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
Find proteins for P04993 (Escherichia coli (strain K12))
Explore P04993 
Go to UniProtKB:  P04993
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UniProt GroupP04993
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-RecBCD protein 2E [auth A]97Salmonella phage P22Mutation(s): 0 
Gene Names: abc2
UniProt
Find proteins for P11191 (Salmonella phage P22)
Explore P11191 
Go to UniProtKB:  P11191
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UniProt GroupP11191
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (70-MER)D [auth X]70synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTREFMAC
MODEL REFINEMENTPHENIX1.17

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom100401/Z/12/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S007261/1
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection, Refinement description