Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 351.71 kDa 
• Atom Count: 23981 
• Modelled Residue Count: 2928 
• Deposited Residue Count: 2982 
• Unique protein chains: 3
• Unique nucleic acid chains: 1

5LD2

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

• DOI: 10.2210/pdb5LD2/pdb
• EMDataResource: EMD-4038

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12, Endothia gyrosa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-06-23 Released: 2016-10-05 
• Deposition Author(s): Wilkinson, M., Chaban, Y., Wigley, D.B.

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Experimental Data Snapshot

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

Literature

Mechanism for nuclease regulation in RecBCD.

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

(2016) Elife 5

• PubMed: 27644322 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB	B	1181	Escherichia coli K-12	Mutation(s): 1  Gene Names: recB, ior, rorA, b2820, JW2788 EC: 3.1.11.5
Find proteins for P08394 (Escherichia coli (strain K12)) Explore P08394  Go to UniProtKB:  P08394

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RecBCD enzyme subunit RecC	C	1122	Escherichia coli K-12	Mutation(s): 0  Gene Names: recC, b2822, JW2790 EC: 3.1.11.5
Find proteins for P07648 (Escherichia coli (strain K12)) Explore P07648  Go to UniProtKB:  P07648

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RecBCD enzyme subunit RecD	D	609	Escherichia coli K-12	Mutation(s): 0  Gene Names: recD, hopE, b2819, JW2787 EC: 3.1.11.5
Find proteins for P04993 (Escherichia coli (strain K12)) Explore P04993  Go to UniProtKB:  P04993

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Fork-Hairpin DNA (70-MER)	X	70	Endothia gyrosa

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	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 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-06-23 
• Released Date: 2016-10-05 
Deposition Author(s): Wilkinson, M., Chaban, Y., Wigley, D.B.

Revision History  

• 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