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 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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

    Howard Hughes Medical Institute, 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: RPA1REPA1RPA70
Find proteins for P27694 (Homo sapiens)
Go to UniProtKB:  P27694
NIH Common Fund Data Resources
PHAROS  P27694
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA replication ATP-dependent helicase/nuclease DNA2
E, F, G, H
13Homo sapiensMutation(s): 0 
Gene Names: DNA2DNA2LKIAA0083
EC: 3.1 (UniProt), 3.6.4.12 (UniProt)
Find proteins for P51530 (Homo sapiens)
Go to UniProtKB:  P51530
NIH Common Fund Data Resources
PHAROS  P51530
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.303α = 90
b = 50.882β = 103.94
c = 76.528γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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