5CNQ | pdb_00005cnq

Crystal structure of the Holliday junction-resolving enzyme GEN1 (WT) in complex with product DNA, Mg2+ and Mn2+ ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.252 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA.

Liu, Y.Freeman, A.D.Declais, A.C.Wilson, T.J.Gartner, A.Lilley, D.M.

(2015) Cell Rep 13: 2565-2575

  • DOI: https://doi.org/10.1016/j.celrep.2015.11.042
  • Primary Citation Related Structures: 
    5CNQ, 5CO8

  • PubMed Abstract: 

    We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction.


  • Organizational Affiliation
    • Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK.

Macromolecule Content 

  • Total Structure Weight: 61.58 kDa 
  • Atom Count: 3,734 
  • Modeled Residue Count: 423 
  • Deposited Residue Count: 495 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclease-like protein464Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0007290
UniProt
Find proteins for G0RYN2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0RYN2 
Go to UniProtKB:  G0RYN2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0RYN2
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RB [auth R]16Escherichia coli
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)-3')C [auth H]15Escherichia coli
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.252 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.582α = 90
b = 98.582β = 90
c = 119.619γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing
iMOSFLMdata reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary