2OBH

Centrin-XPC peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural, thermodynamic, and cellular characterization of human centrin 2 interaction with xeroderma pigmentosum group C protein.

Charbonnier, J.B.Renaud, E.Miron, S.Le Du, M.H.Blouquit, Y.Duchambon, P.Christova, P.Shosheva, A.Rose, T.Angulo, J.F.Craescu, C.T.

(2007) J.Mol.Biol. 373: 1032-1046

  • DOI: 10.1016/j.jmb.2007.08.046

  • PubMed Abstract: 
  • Human centrin 2 (HsCen2), an EF-hand calcium binding protein, plays a regulatory role in the DNA damage recognition during the first steps of the nucleotide excision repair. This biological action is mediated by the binding to a short fragment (N847- ...

    Human centrin 2 (HsCen2), an EF-hand calcium binding protein, plays a regulatory role in the DNA damage recognition during the first steps of the nucleotide excision repair. This biological action is mediated by the binding to a short fragment (N847-R863) from the C-terminal region of xeroderma pigmentosum group C (XPC) protein. This work presents a detailed structural and energetic characterization of the HsCen2/XPC interaction. Using a truncated form of HsCen2 we obtained a high resolution (1.8 A) X-ray structure of the complex with the peptide N847-R863 from XPC. Structural and thermodynamic analysis of the interface revealed the existence of both electrostatic and apolar inter-molecular interactions, but the binding energy is mainly determined by the burial of apolar bulky side-chains into the hydrophobic pocket of the HsCen2 C-terminal domain. Binding studies with various peptide variants showed that XPC residues W848 and L851 constitute the critical anchoring side-chains. This enabled us to define a minimal centrin binding peptide variant of five residues, which accounts for about 75% of the total free energy of interaction between the two proteins. Immunofluorescence imaging in HeLa cells demonstrated that HsCen2 binding to the integral XPC protein may be observed in living cells, and is determined by the same interface residues identified in the X-ray structure of the complex. Overexpression of XPC perturbs the cellular distribution of HsCen2, by inducing a translocation of centrin molecules from the cytoplasm to the nucleus. The present data confirm that the in vitro structural features of the centrin/XPC peptide complex are highly relevant to the cellular context.


    Related Citations: 
    • Flexibility and plasticity of human centrin 2 binding to the xeroderma pigmentosum group C protein (XPC) from nuclear excision repair
      Yang, A.,Miron, S.,Mouawad, L.,Duchambon, P.,Blouquit, Y.,Craescu, C.T.
      (2006) Biochemistry 45: 3653
    • Crystallization and preliminary X-ray diffraction data of the complex between human centrin 2 and a peptide from the protein XPC
      Charbonnier, J.B.,Christova, P.,Shosheva, A.,Le Du, E.,Stura, M.H.,Blouquit, Y.,Duchambon, P.,Miron, S.,Craescu, C.T.
      (2006) Acta Crystallogr.,Sect.F 62: 649
    • The structure of the human centrin 2-xeroderma pigmentosum group C protein complex
      Thompson, J.R.,Ryan, Z.C.,Salisbury, J.L.,Kumar, R.
      (2006) J.Biol.Chem. 281: 18746


    Organizational Affiliation

    Laboratoire de Biologie Structurale et Radiobiologie, iBiTec-S, CEA, Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Centrin-2
A, B
143Homo sapiensMutation(s): 0 
Gene Names: CETN2 (CALT, CEN2)
Find proteins for P41208 (Homo sapiens)
Go to Gene View: CETN2
Go to UniProtKB:  P41208
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-repair protein complementing XP-C cells
C, D
18Homo sapiensMutation(s): 0 
Gene Names: XPC (XPCC)
Find proteins for Q01831 (Homo sapiens)
Go to Gene View: XPC
Go to UniProtKB:  Q01831
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
C, D
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.278α = 90.00
b = 59.419β = 94.67
c = 105.137γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
ADSCdata collection
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-12-19 
  • Released Date: 2007-10-09 
  • Deposition Author(s): Charbonnier, J.B.

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance