5EAN | pdb_00005ean

Crystal structure of Dna2 in complex with a 5' overhang DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.246 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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Literature

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

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

(2015) Elife 4

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

  • 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 2.3 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.

Macromolecule Content 

  • Total Structure Weight: 124.64 kDa 
  • Atom Count: 8,652 
  • Modeled Residue Count: 1,066 
  • Deposited Residue Count: 1,074 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication ATP-dependent helicase/nuclease DNA21,059Mus musculusMutation(s): 0 
Gene Names: Dna2, Dna2l, Kiaa0083
EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
UniProt
Find proteins for Q6ZQJ5 (Mus musculus)
Explore Q6ZQJ5 
Go to UniProtKB:  Q6ZQJ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZQJ5
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)-3')15Mus musculus
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.246 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.153α = 90
b = 118.488β = 90
c = 149.26γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description