4TUG

Crystal structure of MjMre11-DNA2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

DNA end recognition by the Mre11 nuclease dimer: insights into resection and repair of damaged DNA.

Sung, S.Li, F.Park, Y.B.Kim, J.S.Kim, A.K.Song, O.K.Kim, J.Che, J.Lee, S.E.Cho, Y.

(2014) Embo J. 33: 2422-2435

  • DOI: 10.15252/embj.201488299
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Mre11-Rad50-Nbs1 (MRN) complex plays important roles in sensing DNA damage, as well as in resecting and tethering DNA ends, and thus participates in double-strand break repair. An earlier structure of Mre11 bound to a short duplex DNA molecule su ...

    The Mre11-Rad50-Nbs1 (MRN) complex plays important roles in sensing DNA damage, as well as in resecting and tethering DNA ends, and thus participates in double-strand break repair. An earlier structure of Mre11 bound to a short duplex DNA molecule suggested that each Mre11 in a dimer recognizes one DNA duplex to bridge two DNA ends at a short distance. Here, we provide an alternative DNA recognition model based on the structures of Methanococcus jannaschii Mre11 (MjMre11) bound to longer DNA molecules, which may more accurately reflect a broken chromosome. An extended stretch of B-form DNA asymmetrically runs across the whole dimer, with each end of this DNA molecule being recognized by an individual Mre11 monomer. DNA binding induces rigid-body rotation of the Mre11 dimer, which could facilitate melting of the DNA end and its juxtaposition to an active site of Mre11. The identified Mre11 interface binding DNA duplex ends is structurally conserved and shown to functionally contribute to efficient resection, non-homologous end joining, and tolerance to DNA-damaging agents when other resection enzymes are absent. Together, the structural, biochemical, and genetic findings presented here offer new insights into how Mre11 recognizes damaged DNA and facilitates DNA repair.


    Organizational Affiliation

    Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea.,Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea lees4@uthscsa.edu yunje@postech.ac.kr.,Panbionet Corporation, Pohang, South Korea.,Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA lees4@uthscsa.edu yunje@postech.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA double-strand break repair protein Mre11
C, A, B, D, E, F
337Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: mre11
EC: 3.1.-.-
Find proteins for Q58719 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58719
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*AP*CP*GP*TP*AP*GP*GP*AP*CP*AP*GP*C)-3')G14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*TP*GP*TP*CP*CP*TP*AP*CP*GP*TP*GP*CP*CP*A)-3')H15synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.530α = 90.00
b = 185.624β = 99.86
c = 106.212γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-06-24 
  • Released Date: 2014-10-15 
  • Deposition Author(s): Sung, S., Cho, Y.

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Database references