5LD2

Cryo-EM structure of RecBCD+DNA complex revealing activated nuclease domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Mechanism for nuclease regulation in RecBCD.

Wilkinson, M.Chaban, Y.Wigley, D.B.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.18227
  • Primary Citation of Related Structures:  
    5LD2

  • PubMed Abstract: 

    In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is catalysed by AddAB, AdnAB or RecBCD-type helicase-nucleases. These enzyme complexes are highly processive, duplex unwinding and degrading machines that require tight regulation. Here, we report the structure of E.coli RecBCD, determined by cryoEM at 3.8 Å resolution, with a DNA substrate that reveals how the nuclease activity of the complex is activated once unwinding progresses. Extension of the 5'-tail of the unwound duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves a SH3 domain that binds to a region of the RecB subunit in a binding mode that is distinct from others observed previously in SH3 domains and, to our knowledge, this is the first example of peptide-binding of an SH3 domain in a bacterial system.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecBA [auth B]1,181Escherichia coli K-12Mutation(s): 1 
Gene Names: recBiorrorAb2820JW2788
EC: 3.1.11.5
UniProt
Find proteins for P08394 (Escherichia coli (strain K12))
Explore P08394 
Go to UniProtKB:  P08394
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08394
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecCB [auth C]1,122Escherichia coli K-12Mutation(s): 0 
Gene Names: recCb2822JW2790
EC: 3.1.11.5
UniProt
Find proteins for P07648 (Escherichia coli (strain K12))
Explore P07648 
Go to UniProtKB:  P07648
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07648
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecDC [auth D]609Escherichia coli K-12Mutation(s): 0 
Gene Names: recDhopEb2819JW2787
EC: 3.1.11.5
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: 4
MoleculeChains LengthOrganismImage
Fork-Hairpin DNA (70-MER)D [auth X]70Endothia gyrosa
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
E [auth B]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.2: 2019-12-11
    Changes: Other