5DNY

Structure of the ATPrS-Mre11/Rad50-DNA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • 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: mre11, MJ1323
EC: 3.1
UniProt
Find proteins for Q58719 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Go to UniProtKB:  Q58719
Entity Groups  
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UniProt GroupQ58719
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPaseB, D371Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: rad50, MJ1322
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
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (27-MER)E 27synthetic construct
Protein Feature View
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (27-MER)F 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: 0.273 
  • R-Value Work: 0.221 
  • 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
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

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Entry History 

Deposition Data

  • Deposited Date: 2015-09-10 
  • Released Date: 2016-02-24 
    • Deposition Author(s): Liu, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references