3K05

The crystal structure of MDC1 BRCT T2067D in complex with a minimal recognition tetrapeptide with an amidated C-terminus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comparison of the Structures and Peptide Binding Specificities of the BRCT Domains of MDC1 and BRCA1

Campbell, S.J.Edwards, R.A.Glover, J.N.

(2010) Structure 18: 167-176

  • DOI: 10.1016/j.str.2009.12.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The tandem BRCT domains of BRCA1 and MDC1 facilitate protein signaling at DNA damage foci through specific interactions with serine-phosphorylated protein partners. The MDC1 BRCT binds pSer-Gln-Glu-Tyr-COO(-) at the C terminus of the histone variant ...

    The tandem BRCT domains of BRCA1 and MDC1 facilitate protein signaling at DNA damage foci through specific interactions with serine-phosphorylated protein partners. The MDC1 BRCT binds pSer-Gln-Glu-Tyr-COO(-) at the C terminus of the histone variant gammaH2AX via direct recognition of the C-terminal carboxylate, while BRCA1 recognizes pSer-X-X-Phe motifs either at C-terminal or internal sites within target proteins. Using fluorescence polarization binding assays, we show that while both BRCTs prefer a free main chain carboxylate at the +3 position, this preference is much more pronounced in MDC1. Crystal structures of BRCA1 and MDC1 bound to tetrapeptide substrates reveal differences in the environment of conserved arginines (Arg1699 in BRCA1 and Arg1933 in MDC1) that determine the relative affinity for peptides with -COO(-) versus -CO-NH(2) termini. A mutation in MDC1 that induces a more BRCA1-like conformation relaxes the binding specificity, allowing the mutant to bind phosphopeptides lacking a -COO(-) terminus.


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mediator of DNA damage checkpoint protein 1
A, B
200Homo sapiensMutation(s): 1 
Gene Names: MDC1 (KIAA0170, NFBD1)
Find proteins for Q14676 (Homo sapiens)
Go to Gene View: MDC1
Go to UniProtKB:  Q14676
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
phospho peptide
C, D
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
C, D
NON-POLYMERH2 N

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SEP
Query on SEP
C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.642α = 90.00
b = 74.580β = 90.00
c = 103.408γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data collection
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description