Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 10.44 kDa 
• Atom Count: 974 
• Residue Count: 92 
• Unique protein chains: 1

4QBO

VRR_NUC domain

• DOI: 10.2210/pdb4QBO/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus phage P9
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-08 Released: 2014-09-10 
• Deposition Author(s): Smerdon, S.J., Pennell, S., Li, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.180 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

Literature

FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain.

Pennell, S., Declais, A.C., Li, J., Haire, L.F., Berg, W., Saldanha, J.W., Taylor, I.A., Rouse, J., Lilley, D.M., Smerdon, S.J.

(2014) Cell Rep 8: 84-93

• PubMed: 24981866 
• DOI: 10.1016/j.celrep.2014.06.001
• Primary Citation of Related Structures:  
  4QBN, 4QBO, 4QBL


• PubMed Abstract: 
  

FAN1 is a structure-selective DNA repair nuclease with 5' flap endonuclease activity, involved in the repair of interstrand DNA crosslinks. It is the only eukaryotic protein with a virus-type replication-repair nuclease ("VRR-Nuc") "module" that commonly occurs as a standalone domain in many bacteria and viruses. Crystal structures of three representatives show that they structurally resemble Holliday junction resolvases (HJRs), are dimeric in solution, and are able to cleave symmetric four-way junctions. In contrast, FAN1 orthologs are monomeric and cleave 5' flap structures in vitro, but not Holliday junctions. Modeling of the VRR-Nuc domain of FAN1 reveals that it has an insertion, which packs against the dimerization interface observed in the structures of the viral/bacterial VRR-Nuc proteins. We propose that these additional structural elements in FAN1 prevent dimerization and bias specificity toward flap structures.

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Organizational Affiliation: 

Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease	A	92	Streptococcus phage P9	Mutation(s): 0
Find proteins for A7J283 (Streptococcus phage P9) Explore A7J283  Go to UniProtKB:  A7J283

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.180 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.854	α = 90
b = 60.517	β = 90
c = 81.137	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-08 
• Released Date: 2014-09-10 
Deposition Author(s): Smerdon, S.J., Pennell, S., Li, J.

Revision History 

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description