2I0Q

Crystal structure of a telomere single-strand DNA-protein complex from O. nova with full-length alpha and beta telomere proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural reorganization and the cooperative binding of single-stranded telomere DNA in Sterkiella nova.

Buczek, P.Horvath, M.P.

(2006) J.Biol.Chem. 281: 40124-40134

  • DOI: 10.1074/jbc.M607749200

  • PubMed Abstract: 
  • In Sterkiella nova, alpha and beta telomere proteins bind cooperatively with single-stranded DNA to form a ternary alpha.beta.DNA complex. Association of telomere protein subunits is DNA-dependent, and alpha-beta association enhances DNA affinity. To ...

    In Sterkiella nova, alpha and beta telomere proteins bind cooperatively with single-stranded DNA to form a ternary alpha.beta.DNA complex. Association of telomere protein subunits is DNA-dependent, and alpha-beta association enhances DNA affinity. To further understand the molecular basis for binding cooperativity, we characterized several possible stepwise assembly pathways using isothermal titration calorimetry. In one path, alpha and DNA first form a stable alpha.DNA complex followed by the addition of beta in a second step. Binding energy accumulates with nearly equal free energy of association for each of these steps. Heat capacity is nonetheless dramatically different, with DeltaCp = -305 +/- 3 cal mol(-1) K(-1) for alpha binding with DNA and DeltaCp = -2010 +/- 20 cal mol(-1) K(-1) for the addition of beta to complete the alpha.beta.DNA complex. By examining alternate routes including titration of single-stranded DNA with a preformed alpha.beta complex, a significant portion of binding energy and heat capacity could be assigned to structural reorganization involving protein-protein interactions and repositioning of the DNA. Structural reorganization probably affords a mechanism to regulate high affinity binding of telomere single-stranded DNA with important implications for telomere biology. Regulation of telomere complex dissociation is thought to involve post-translational modifications in the lysine-rich C-terminal portion of beta. We observed no difference in binding energetics or crystal structure when comparing complexes prepared with full-length beta or a C-terminally truncated form, supporting interesting parallels between the intrinsically disordered regions of histones and this portion of beta.


    Related Citations: 
    • Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA
      Horvath, M.P.,Schweiker, V.L.,Bevilacqua, J.M.,Ruggles, J.A.,Schultz, S.C.
      (1998) Cell 95: 963
    • DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex
      Horvath, M.P.,Schultz, S.C.
      (2001) J.Mol.Biol. 310: 367


    Organizational Affiliation

    Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Telomere-binding protein alpha subunit
A
495Sterkiella novaMutation(s): 0 
Gene Names: MAC-56A, MAC-56K, MAC-56S
Find proteins for P29549 (Sterkiella nova)
Go to UniProtKB:  P29549
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Telomere-binding protein beta subunit
B
385Sterkiella novaMutation(s): 0 
Gene Names: MAC-41A, MAC-41S
Find proteins for P16458 (Sterkiella nova)
Go to UniProtKB:  P16458
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'D11N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.243 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.331α = 90.00
b = 93.331β = 90.00
c = 423.779γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSphasing
CNSrefinement
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance