2ADO

Crystal Structure Of The Brct Repeat Region From The Mediator of DNA damage checkpoint protein 1, MDC1

• PDB DOI: https://doi.org/10.2210/pdb2ADO/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-07-20 Released: 2005-08-02 
• Deposition Author(s): Lee, M.S., Edwards, R.A., Thede, G.L., Glover, J.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.212 
• R-Value Work: 0.195 

Literature

Structure of the BRCT Repeat Domain of MDC1 and Its Specificity for the Free COOH-terminal End of the {gamma}-H2AX Histone Tail.

Lee, M.S., Edwards, R.A., Thede, G.L., Glover, J.N.

(2005) J Biol Chem 280: 32053-32056

• PubMed: 16049003 
• DOI: https://doi.org/10.1074/jbc.C500273200
• Primary Citation of Related Structures:  
  2ADO


• PubMed Abstract: 
  

  MDC1 (mediator of DNA damage checkpoint protein 1) regulates the recognition and repair of DNA double strand breaks in mammalian cells through its interactions with nuclear foci containing the COOH-terminally phosphorylated form of the histone variant, H2AX. Here we demonstrate that the tandem BRCT repeats of MDC1 directly bind to the phosphorylated tail of H2AX-Ser(P)-Gln-Glu-Tyr, in a manner that is critically dependent on the free carboxylate group of the COOH-terminal Tyr residue. We have determined the x-ray crystal structure of the MDC1 BRCT repeats at 1.45 Angstroms resolution. By a comparison with the structure of the BRCA1 BRCT bound to a phosphopeptide, we suggest that two arginine residues in MDC1, Arg(1932) and Arg(1933) may recognize the COOH terminus of the peptide as well as the penultimate Glu of H2AX, while Gln(2013) may provide additional specificity for the COOH-terminal Tyr.

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Organizational Affiliation: 

Department of Biochemistry, University of Alberta, Edmonton, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.02 kDa 
• Atom Count: 3,255 
• Modelled Residue Count: 389 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of DNA damage checkpoint protein 1	A, B	196	Homo sapiens	Mutation(s): 0  Gene Names: MDC1, KIAA0170, NFBD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14676 (Homo sapiens) Explore Q14676  Go to UniProtKB:  Q14676
PHAROS:  Q14676 GTEx:  ENSG00000137337

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.212 
• R-Value Work: 0.195 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.051	α = 72.95
b = 44.44	β = 87.54
c = 61.942	γ = 61.8

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-02 
Deposition Author(s): Lee, M.S., Edwards, R.A., Thede, G.L., Glover, J.N.

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references