4HJ7

Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTAGGGT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.783 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes.

Dickey, T.H.McKercher, M.A.Wuttke, D.S.

(2013) Structure 21: 121-132

  • DOI: 10.1016/j.str.2012.10.015
  • Primary Citation of Related Structures:  4HID, 4HIK, 4HIM, 4HIO, 4HJ5, 4HJ8, 4HJ9, 4HJA

  • PubMed Abstract: 
  • Pot1 is the protein responsible for binding to and protecting the 3' single-stranded DNA (ssDNA) overhang at most eukaryotic telomeres. Here, we present the crystal structure of one of the two oligonucleotide/oligosaccharide-binding folds (Pot1pC) th ...

    Pot1 is the protein responsible for binding to and protecting the 3' single-stranded DNA (ssDNA) overhang at most eukaryotic telomeres. Here, we present the crystal structure of one of the two oligonucleotide/oligosaccharide-binding folds (Pot1pC) that make up the ssDNA-binding domain in S. pombe Pot1. Comparison with the homologous human domain reveals unexpected structural divergence in the mode of ligand binding that explains the differing ligand requirements between species. Despite the presence of apparently base-specific hydrogen bonds, Pot1pC is able to bind a wide range of ssDNA sequences with thermodynamic equivalence. To address how Pot1pC binds ssDNA with little to no specificity, multiple structures of Pot1pC bound to noncognate ssDNA ligands were solved. These structures reveal that this promiscuity is implemented through new binding modes that thermodynamically compensate for base-substitutions through alternate stacking interactions and new H-bonding networks.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protection of telomeres protein 1
A
143Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: pot1
Find proteins for O13988 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O13988
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*TP*TP*AP*GP*GP*GP*T)-3')B9Schizosaccharomyces pombe 972h-
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.783 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.756α = 90.00
b = 58.181β = 90.00
c = 65.626γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data collection
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description