4W9M

AMPPNP bound Rad50 in complex with dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of the Rad50 DNA double-strand break repair protein in complex with DNA.

Rojowska, A.Lammens, K.Seifert, F.U.Direnberger, C.Feldmann, H.Hopfner, K.P.

(2014) EMBO J 33: 2847-2859

  • DOI: 10.15252/embj.201488889
  • Primary Citation of Related Structures:  
    4W9M

  • PubMed Abstract: 
  • The Mre11-Rad50 nuclease-ATPase is an evolutionarily conserved multifunctional DNA double-strand break (DSB) repair factor. Mre11-Rad50's mechanism in the processing, tethering, and signaling of DSBs is unclear, in part because we lack a structural framework for its interaction with DNA in different functional states ...

    The Mre11-Rad50 nuclease-ATPase is an evolutionarily conserved multifunctional DNA double-strand break (DSB) repair factor. Mre11-Rad50's mechanism in the processing, tethering, and signaling of DSBs is unclear, in part because we lack a structural framework for its interaction with DNA in different functional states. We determined the crystal structure of Thermotoga maritima Rad50(NBD) (nucleotide-binding domain) in complex with Mre11(HLH) (helix-loop-helix domain), AMPPNP, and double-stranded DNA. DNA binds between both coiled-coil domains of the Rad50 dimer with main interactions to a strand-loop-helix motif on the NBD. Our analysis suggests that this motif on Rad50 does not directly recognize DNA ends and binds internal sites on DNA. Functional studies reveal that DNA binding to Rad50 is not critical for DNA double-strand break repair but is important for telomere maintenance. In summary, we provide a structural framework for DNA binding to Rad50 in the ATP-bound state.


    Organizational Affiliation

    Department of Biochemistry and Gene Center, Ludwig-Maximilians-University, Munich, Germany Center for Integrated Protein Sciences, Munich, Germany hopfner@genzentrum.lmu.de.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPaseC, E, I, K365Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: rad50TM_1636
UniProt
Find proteins for Q9X1X1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1X1 
Go to UniProtKB:  Q9X1X1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exonuclease, putativeD, F, J, L37Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: TM_1635THEMA_06070sbcD
UniProt
Find proteins for Q9X1X0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1X0 
Go to UniProtKB:  Q9X1X0
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*GP*AP*CP*CP*GP*AP*CP*C)-3')A [auth Y], G [auth Z]15synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*CP*AP*CP*CP*GP*AP*CP*C)-3')B [auth A], H [auth G]15synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.70 Å
      • R-Value Free: 0.270 
      • R-Value Work: 0.215 
      • R-Value Observed: 0.218 
      • Space Group: P 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 49.713α = 90.01
      b = 96.386β = 89.22
      c = 105.926γ = 81.67
      Software Package:
      Software NamePurpose
      XDSdata reduction
      XSCALEdata scaling
      PHENIXrefinement
      PDB_EXTRACTdata extraction
      PHASERphasing
      XSCALEdata reduction

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2015-01-14
        Type: Initial release
      • Version 1.1: 2015-02-25
        Changes: Other
      • Version 2.0: 2018-10-24
        Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy