5T9J

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    5T9J

  • 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 resolva ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Flap endonuclease GEN homolog 1 AB506Homo sapiensMutation(s): 3 
Gene Names: GEN1
EC: 3.1
Find proteins for Q17RS7 (Homo sapiens)
Explore Q17RS7 
Go to UniProtKB:  Q17RS7
NIH Common Fund Data Resources
PHAROS:  Q17RS7
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    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
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      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
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        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
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 5
          MoleculeChainsLengthOrganismImage
          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
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 3.00 Å
          • R-Value Free: 0.241 
          • R-Value Work: 0.199 
          • R-Value Observed: 0.201 
          • Space Group: P 32
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 86.94α = 90
          b = 86.94β = 90
          c = 200.724γ = 120
          Software Package:
          Software NamePurpose
          autoSHARPphasing
          PHENIXrefinement
          PDB_EXTRACTdata extraction
          XDSdata reduction
          XDSdata scaling

          Structure Validation

          View Full Validation Report



          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