4HIK

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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: https://doi.org/10.1016/j.str.2012.10.015
  • Primary Citation of Related Structures:  
    4HID, 4HIK, 4HIM, 4HIO, 4HJ5, 4HJ7, 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) that make up the ssDNA-binding domain in S ...

    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. Electronic address: deborah.wuttke@colorado.edu.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protection of telomeres protein 1143Schizosaccharomyces pombe 972h-Mutation(s): 1 
Gene Names: pot1, SPAC26H5.06
UniProt
Find proteins for O13988 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13988 
Go to UniProtKB:  O13988
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13988
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*TP*TP*AP*CP*GP*GP*T)-3')9Schizosaccharomyces pombe 972h-
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.87α = 90
b = 57.39β = 90
c = 66.17γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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