5USO

Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera (GGTTACrGrGrU)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Discrimination against RNA Backbones by a ssDNA Binding Protein.

Lloyd, N.R.Wuttke, D.S.

(2018) Structure 26: 722-733.e2

  • DOI: https://doi.org/10.1016/j.str.2018.03.016
  • Primary Citation of Related Structures:  
    5USB, 5USN, 5USO

  • PubMed Abstract: 

    Pot1 is the shelterin component responsible for the protection of the single-stranded DNA (ssDNA) overhang at telomeres in nearly all eukaryotic organisms. The C-terminal domain of the DNA-binding domain, Pot1pC, exhibits non-specific ssDNA recognition, achieved through thermodynamically equivalent alternative binding conformations. Given this flexibility, it is unclear how specificity for ssDNA over RNA, an activity required for biological function, is achieved. Examination of the ribose-position specificity of Pot1pC shows that ssDNA specificity is additive but not uniformly distributed across the ligand. High-resolution structures of several Pot1pC complexes with RNA-DNA chimeric ligands reveal Pot1pC discriminates against RNA by utilizing non-compensatory binding modes that feature significant rearrangement of the binding interface. These alternative conformations, accessed through both ligand and protein flexibility, recover much, but not all, of the binding energy, leading to the observed reduction in affinities. These findings suggest that intermolecular interfaces are remarkably sophisticated in their tuning of specificity toward flexible ligands.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado, UCB 596, Boulder, CO 80309-0596, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protection of telomeres protein 1139Schizosaccharomyces pombeMutation(s): 1 
Gene Names: pot1
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
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
7-9R_9mer DNA/RNA (5'-D(*GP*GP*TP*TP*AP*C)-R(P*GP*GP*U)-3')9Schizosaccharomyces pombe
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.56α = 90
b = 57.61β = 90
c = 66.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOSFLMdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB1121842
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM-065103
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM059414

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.4: 2024-04-03
    Changes: Refinement description