5F3W

Structure of the ATPrS-Mre11/Rad50-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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Literature

ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex

Liu, Y.Sung, S.Kim, Y.Li, F.Gwon, G.Jo, A.Kim, A.K.Kim, T.Song, O.K.Lee, S.E.Cho, Y.

(2016) EMBO J 35: 743-758

  • DOI: 10.15252/embj.201592462
  • Primary Citation of Related Structures:  
    5DNY, 5F3W

  • PubMed Abstract: 
  • ATP-dependent DNA end recognition and nucleolytic processing are central functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair. However, it is still unclear how ATP binding and hydrolysis primes the MR function and regulates repair pathway choice in cells ...

    ATP-dependent DNA end recognition and nucleolytic processing are central functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair. However, it is still unclear how ATP binding and hydrolysis primes the MR function and regulates repair pathway choice in cells. Here,Methanococcus jannaschii MR-ATPγS-DNA structure reveals that the partly deformed DNA runs symmetrically across central groove between two ATPγS-bound Rad50 nucleotide-binding domains. Duplex DNA cannot access the Mre11 active site in the ATP-free full-length MR complex. ATP hydrolysis drives rotation of the nucleotide-binding domain and induces the DNA melting so that the substrate DNA can access Mre11. Our findings suggest that the ATP hydrolysis-driven conformational changes in both DNA and the MR complex coordinate the melting and endonuclease activity.


    Organizational Affiliation

    Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea yunje@postech.ac.kr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA double-strand break repair protein Mre11A, C386Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: mre11MJ1323
EC: 3.1
UniProt
Find proteins for Q58719 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58719 
Go to UniProtKB:  Q58719
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58719
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPaseB, D372Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: rad50MJ1322
UniProt
Find proteins for Q58718 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58718 
Go to UniProtKB:  Q58718
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58718
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
27-MER DNAE 27synthetic construct
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
27-MER DNAF 27synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
I [auth B],
L [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth C],
K [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.303α = 90
b = 130.111β = 90
c = 166.656γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-12-03 
  • Released Date: 2016-03-02 
  • Deposition Author(s): Liu, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-04-13
    Changes: Database references