5EAY

Crystal structure of a Dna2 peptide in complex with Rpa 70N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.232 

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:  

  • 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 polar ...

    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

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replication protein A 70 kDa DNA-binding subunit
A, B, C, D
118Homo sapiensMutation(s): 0 
Gene Names: RPA1 (REPA1, RPA70)
Find proteins for P27694 (Homo sapiens)
Go to Gene View: RPA1
Go to UniProtKB:  P27694
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA replication ATP-dependent helicase/nuclease DNA2
E, F, G, H
13Homo sapiensMutation(s): 0 
Gene Names: DNA2 (DNA2L, KIAA0083)
Find proteins for P51530 (Homo sapiens)
Go to Gene View: DNA2
Go to UniProtKB:  P51530
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.303α = 90.00
b = 50.882β = 103.94
c = 76.528γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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