6SJF | pdb_00006sjf

Cryo-EM structure of the RecBCD Chi unrecognised complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair.

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

(2020) Nat Struct Mol Biol 27: 71-77

  • DOI: https://doi.org/10.1038/s41594-019-0355-2
  • Primary Citation Related Structures: 
    6SJB, 6SJE, 6SJF, 6SJG, 6T2U, 6T2V

  • PubMed Abstract: 

    The RecBCD complex plays key roles in phage DNA degradation, CRISPR array acquisition (adaptation) and host DNA repair. The switch between these roles is regulated by a DNA sequence called Chi. We report cryo-EM structures of the Escherichia coli RecBCD complex bound to several different DNA forks containing a Chi sequence, including one in which Chi is recognized and others in which it is not. The Chi-recognized structure shows conformational changes in regions of the protein that contact Chi and reveals a tortuous path taken by the DNA. Sequence specificity arises from interactions with both the RecC subunit and the sequence itself. These structures provide molecular details for how Chi is recognized and insights into the changes that occur in response to Chi binding that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition to constructive host DNA repair.


  • Organizational Affiliation
    • Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.

Macromolecule Content 

  • Total Structure Weight: 356.25 kDa 
  • Atom Count: 23,826 
  • Modeled Residue Count: 2,901 
  • Deposited Residue Count: 2,996 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RecBCD enzyme subunit RecBA [auth B]1,181Escherichia coliMutation(s): 1 
Gene Names: recBiorrorAb2820JW2788
EC: 3.1.11.5 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for P08394 (Escherichia coli (strain K12))
Explore P08394 
Go to UniProtKB:  P08394
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UniProt GroupP08394
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Reference Sequence
Find similar proteins by:|  3D Structure
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))
Explore P07648 
Go to UniProtKB:  P07648
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UniProt GroupP07648
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Entity Groups
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UniProt GroupP04993
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 4
MoleculeChains LengthOrganismImage
Forked DNA substrateD [auth X]85synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.12

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection, Database references, Refinement description