5EAX

Crystal structure of Dna2 in complex with an ssDNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.

Zhou, C., Pourmal, S., Pavletich, N.P.

(2015) Elife 4

  • DOI: 10.7554/eLife.09832
  • Primary Citation of Related Structures:  
    5EAN, 5EAY, 5EAX, 5EAW

  • PubMed Abstract: 

    • The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2 ...

    The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5' end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5' but not 3' end, explaining how Rpa regulates cleavage polarity.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, United States.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication ATP-dependent helicase/nuclease DNA2 A, B1056Mus musculusMutation(s): 1 
Gene Names: Dna2, Dna2l, Kiaa0083
EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
Find proteins for Q6ZQJ5 (Mus musculus)
Explore Q6ZQJ5 
Go to UniProtKB:  Q6ZQJ5
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')E, H17synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP
    Download Ideal Coordinates CCD File 
    A, B
    		ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N    		 Ligand Interaction
    SF4
    Query on SF4
    Download Ideal Coordinates CCD File 
    A, B
    		IRON/SULFUR CLUSTER
    Fe4 S4
    LJBDFODJNLIPKO-VKOJMFJBAC    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.05 Å
    • R-Value Free: 0.256 
    • R-Value Work: 0.223 
    • R-Value Observed: 0.223 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 120.234α = 90
    b = 149.211β = 90
    c = 172.9γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    SCALEPACKdata scaling
    PDB_EXTRACTdata extraction
    PHASERphasing
    HKL-2000data reduction

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2015-11-18
      Type: Initial release