2OBH

Centrin-XPC peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

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
  • Primary Citation of Related Structures:  
    2OBH

  • 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-R863) from the C-terminal region of xeroderma pigmentosum group C (XPC) protein ...

    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: 
    • 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 Struct Biol Cryst Commun 62: 649
    • 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
    • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Centrin-2A, B143Homo sapiensMutation(s): 0 
Gene Names: CETN2CALTCEN2
UniProt & NIH Common Fund Data Resources
Find proteins for P41208 (Homo sapiens)
Explore P41208 
Go to UniProtKB:  P41208
PHAROS:  P41208
GTEx:  ENSG00000147400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41208
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-repair protein complementing XP-C cellsC, D18N/AMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q01831 (Homo sapiens)
Explore Q01831 
Go to UniProtKB:  Q01831
PHAROS:  Q01831
GTEx:  ENSG00000154767 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01831
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.278α = 90
b = 59.419β = 94.67
c = 105.137γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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