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 

wwPDB Validation   3D Report Full Report


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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB B1181Escherichia coli K-12Mutation(s): 1 
Gene Names: recBiorrorAb2820JW2788
EC: 3.1.11.5
Find proteins for P08394 (Escherichia coli (strain K12))
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Go to UniProtKB:  P08394
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecC C1122Escherichia coli K-12Mutation(s): 0 
Gene Names: recCb2822JW2790
EC: 3.1.11.5
Find proteins for P07648 (Escherichia coli (strain K12))
Explore P07648 
Go to UniProtKB:  P07648
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecD D609Escherichia coli K-12Mutation(s): 0 
Gene Names: recDhopEb2819JW2787
EC: 3.1.11.5
Find proteins for P04993 (Escherichia coli (strain K12))
Explore P04993 
Go to UniProtKB:  P04993
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
Fork-Hairpin DNA (70-MER)X70Endothia gyrosa
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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