Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.42 kDa 
• Atom Count: 2979 
• Modelled Residue Count: 321 
• Deposited Residue Count: 322 
• Unique protein chains: 2

2OBH

Centrin-XPC peptide

• PDB DOI: 10.2210/pdb2OBH/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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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 

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

• PubMed: 17897675 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centrin-2	A, B	143	Homo sapiens	Mutation(s): 0  Gene Names: CETN2, CALT, CEN2
UniProt & NIH Common Fund Data Resources
Find proteins for P41208 (Homo sapiens) Explore P41208  Go to UniProtKB:  P41208
PHAROS:  P41208 GTEx:  ENSG00000147400

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-repair protein complementing XP-C cells	C, D	18	N/A	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q01831 (Homo sapiens) Explore Q01831  Go to UniProtKB:  Q01831
PHAROS:  Q01831 GTEx:  ENSG00000154767

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 60.278	α = 90
b = 59.419	β = 94.67
c = 105.137	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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
  Changes: Advisory, Version format compliance