1KIX | pdb_00001kix

Dimeric Structure of the O. nova Telomere End Binding Protein Alpha Subunit with Bound ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.240 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Dimeric structure of the Oxytricha nova telomere end-binding protein alpha-subunit bound to ssDNA.

Peersen, O.B.Ruggles, J.A.Schultz, S.C.

(2002) Nat Struct Biol 9: 182-187

  • DOI: https://doi.org/10.1038/nsb761
  • Primary Citation Related Structures: 
    1KIX

  • PubMed Abstract: 

    Telomeres are the specialized protein--DNA complexes that cap and protect the ends of linear eukaryotic chromosomes. The extreme 3' end of the telomeric DNA in Oxytricha nova is bound by a two-subunit sequence-specific and 3' end-specific protein called the telomere end-binding protein (OnTEBP). Here we describe the crystal structure of the alpha-subunit of OnTEBP in complex with T4G4 single-stranded telomeric DNA. This structure shows an (alpha--ssDNA)2 homodimer with a large approximately 7,000 A2 protein--protein interface in which the domains of alpha are rearranged extensively from their positions in the structure of an alpha--beta--ssDNA ternary complex. The (alpha--ssDNA)2 complex can bind two telomeres on opposite sides of the dimer and, thus, acts as a protein mediator of telomere--telomere associations. The structures of the (alpha--ssDNA)2 dimer presented here and the previously described alpha--beta--ssDNA complex demonstrate that OnTEBP forms multiple telomeric complexes that potentially mediate the assembly and disassembly of higher order telomeric structures.


  • Organizational Affiliation
    • University of Colorado, Department of Chemistry and Biochemistry, Boulder, Colorado 80309-0215 USA. Olve.Peersen@ColoState.edu

Macromolecule Content 

  • Total Structure Weight: 58.85 kDa 
  • Atom Count: 3,837 
  • Modeled Residue Count: 453 
  • Deposited Residue Count: 503 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Telomere-Binding Protein alpha SubunitB [auth A]495Sterkiella novaMutation(s): 0 
Gene Names: MAC-56A
UniProt
Find proteins for P29549 (Sterkiella nova)
Explore P29549 
Go to UniProtKB:  P29549
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29549
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*T*TP*TP*TP*GP*GP*GP*G)-3'A [auth D]8N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.240 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 284α = 90
b = 284β = 90
c = 284γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description