1PH6

Crystal Structure of THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGTGG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes

Theobald, D.L.Schultz, S.C.

(2003) Embo J. 22: 4314-4324

  • DOI: 10.1093/emboj/cdg415
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore ...

    Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore the mechanisms of sequence-specific ssDNA recognition, we determined the crystal structures of 10 different non-cognate ssDNAs complexed with the Oxytricha nova telomere end-binding protein (OnTEBP) and evaluated their corresponding binding affinities (PDB ID codes 1PH1-1PH9 and 1PHJ). The thermodynamic and structural effects of these sequence perturbations could not have been predicted based solely upon the cognate structure. OnTEBP accommodates non-cognate nucleotides by both subtle adjustments and surprisingly large structural rearrangements in the ssDNA. In two complexes containing ssDNA intermediates that occur during telomere extension by telomerase, entire nucleotides are expelled from the complex. Concurrently, the sequence register of the ssDNA shifts to re-establish a more cognate-like pattern. This phenomenon, termed nucleotide shuffling, may be of general importance in protein recognition of single-stranded nucleic acids. This set of structural and thermodynamic data highlights a fundamental difference between protein recognition of ssDNA versus dsDNA.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA. theobal@colorado.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Telomere-binding protein alpha subunit
A
461Sterkiella novaMutation(s): 0 
Gene Names: MAC-56A, MAC-56K, MAC-56S
Find proteins for P29549 (Sterkiella nova)
Go to UniProtKB:  P29549
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Telomere-binding protein beta subunit
B
217Sterkiella 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*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3'G,H13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*TP*GP*G)-3'D11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.465α = 90.00
b = 93.465β = 90.00
c = 423.944γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance