3PXA

Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Impact of BRCA1 BRCT Domain Missense Substitutions on Phosphopeptide Recognition.

Coquelle, N.Green, R.Glover, J.N.

(2011) Biochemistry 50: 4579-4589

  • DOI: https://doi.org/10.1021/bi2003795
  • Primary Citation of Related Structures:  
    3PXA, 3PXB, 3PXC, 3PXD, 3PXE

  • PubMed Abstract: 
  • The BRCA1 BRCT domain binds pSer-x-x-Phe motifs in partner proteins to regulate the cellular response to DNA damage. Approximately 120 distinct missense variants have been identified in the BRCA1 BRCT through breast cancer screening, and several of these have been linked to an increased cancer risk ...

    The BRCA1 BRCT domain binds pSer-x-x-Phe motifs in partner proteins to regulate the cellular response to DNA damage. Approximately 120 distinct missense variants have been identified in the BRCA1 BRCT through breast cancer screening, and several of these have been linked to an increased cancer risk. Here we probe the structures and peptide-binding activities of variants that affect the BRCA1 BRCT phosphopeptide-binding groove. The results obtained from the G1656D and T1700A variants illustrate the role of Ser1655 in pSer recognition. Mutations at Arg1699 (R1699W and R1699Q) significantly reduce peptide binding through loss of contacts to the main chain of the Phe(+3) residue and, in the case of R1699W, to a destabilization of the BRCT fold. The R1835P and E1836K variants do not dramatically reduce peptide binding, in spite of the fact that these mutations significantly alter the structure of the walls of the Phe(+3) pocket.


    Related Citations: 
    • Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays.
      Lee, M.S., Green, R., Marsillac, S.M., Coquelle, N., Williams, R.S., Yeung, T., Foo, D., Hau, D.D., Hui, B., Monteiro, A.N., Glover, J.N.
      (2010) Cancer Res 70: 4880
    • Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1.
      Williams, R.S., Lee, M.S., Hau, D.D., Glover, J.N.
      (2004) Nat Struct Mol Biol 11: 519
    • Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer.
      Clapperton, J.A., Manke, I.A., Lowery, D.M., Ho, T., Haire, L.F., Yaffe, M.B., Smerdon, S.J.
      (2004) Nat Struct Mol Biol 11: 512
    • Structural consequences of a cancer-causing BRCA1-BRCT missense mutation.
      Williams, R.S., Glover, J.N.
      (2003) J Biol Chem 278: 2630

    Organizational Affiliation

    Department of Biochemistry, School of Medicine, University of Alberta, Edmonton, AB, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Breast cancer type 1 susceptibility protein214Homo sapiensMutation(s): 1 
Gene Names: BRCA1RNF53
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P38398 (Homo sapiens)
Explore P38398 
Go to UniProtKB:  P38398
PHAROS:  P38398
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38398
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.87α = 90
b = 114.87β = 90
c = 122.11γ = 120
Software Package:
Software NamePurpose
MxDCdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description