4QBO | pdb_00004qbo

VRR_NUC domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.180 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.172 (Depositor) 
  • R-Value Observed: 
    0.172 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

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

  • DOI: https://doi.org/10.1016/j.celrep.2014.06.001
  • Primary Citation Related Structures: 
    4QBL, 4QBN, 4QBO

  • 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.


  • Organizational Affiliation
    • Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK. Electronic address: spennel@nimr.mrc.ac.uk.

Macromolecule Content 

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

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclease92Streptococcus phage P9Mutation(s): 0 
UniProt
Find proteins for A0ACD6B8D9 (Streptococcus phage P9)
Explore A0ACD6B8D9 
Go to UniProtKB:  A0ACD6B8D9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B8D9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth 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 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.172 (Depositor) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.854α = 90
b = 60.517β = 90
c = 81.137γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations