5T9J

Crystal Structure of human GEN1 in complex with Holliday junction DNA in the upper interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00013 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage.

Lee, S.H.Princz, L.N.Klugel, M.F.Habermann, B.Pfander, B.Biertumpfel, C.

(2015) Elife 4: --

  • DOI: 10.7554/eLife.12256

  • PubMed Abstract: 
  • Holliday junctions (HJs) are key DNA intermediates in homologous recombination. They link homologous DNA strands and have to be faithfully removed for proper DNA segregation and genome integrity. Here, we present the crystal structure of human HJ res ...

    Holliday junctions (HJs) are key DNA intermediates in homologous recombination. They link homologous DNA strands and have to be faithfully removed for proper DNA segregation and genome integrity. Here, we present the crystal structure of human HJ resolvase GEN1 complexed with DNA at 3.0 Å resolution. The GEN1 core is similar to other Rad2/XPG nucleases. However, unlike other members of the superfamily, GEN1 contains a chromodomain as an additional DNA interaction site. Chromodomains are known for their chromatin-targeting function in chromatin remodelers and histone(de)acetylases but they have not previously been found in nucleases. The GEN1 chromodomain directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. Structure-guided mutations in vitro and in vivo in yeast validated our mechanistic findings. Our study provides the missing structure in the Rad2/XPG family and insights how a well-conserved nuclease core acquires versatility in recognizing diverse substrates for DNA repair and maintenance.


    Organizational Affiliation

    Department of Structural Cell Biology, Molecular Mechanisms of DNA Repair, Max Planck Institute of Biochemistry, Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flap endonuclease GEN homolog 1
A, B
506Homo sapiensMutation(s): 1 
Gene Names: GEN1
EC: 3.1.-.-
Find proteins for Q17RS7 (Homo sapiens)
Go to Gene View: GEN1
Go to UniProtKB:  Q17RS7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DGP*DC)-3')C20synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DCP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DAP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DT)-3')D20synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DCP*DTP*DC)-3')E20synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DAP*DGP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DTP*DCP*DCP*DGP*DGP*DAP*DAP*DTP*DTP*DC)-3')F20synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00013 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 86.940α = 90.00
b = 86.940β = 90.00
c = 200.724γ = 120.00
Software Package:
Software NamePurpose
autoSHARPphasing
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermanyMax Planck Research Group Leader Program

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release