3KJO

Crystal Structure of hPOT1V2-dTrUd(AGGGTTAG)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

How telomeric protein POT1 avoids RNA to achieve specificity for single-stranded DNA.

Nandakumar, J., Podell, E.R., Cech, T.R.

(2010) Proc Natl Acad Sci U S A 107: 651-656

  • DOI: 10.1073/pnas.0911099107
  • Primary Citation of Related Structures:  
    3KJO, 3KJP

  • PubMed Abstract: 

    • The POT1-TPP1 heterodimer, the major telomere-specific single-stranded DNA-binding protein in mammalian cells, protects chromosome ends and contributes to the regulation of telomerase. The recent discovery of telomeric RNA raises the question of how POT1 faithfully binds telomeric ssDNA and avoids illicit RNA binding that could result in its depletion from telomeres ...

    The POT1-TPP1 heterodimer, the major telomere-specific single-stranded DNA-binding protein in mammalian cells, protects chromosome ends and contributes to the regulation of telomerase. The recent discovery of telomeric RNA raises the question of how POT1 faithfully binds telomeric ssDNA and avoids illicit RNA binding that could result in its depletion from telomeres. Here we show through binding studies that a single deoxythymidine in a telomeric repeat dictates the DNA versus RNA discrimination by human POT1 and mouse POT1A. We solve the crystal structure of hPOT1 bound to DNA with a ribouridine in lieu of the critical deoxythymidine and show that this substitution results in burying the 2(')-hydroxyl group in a hydrophobic region (Phe62) of POT1 in addition to eliminating favorable hydrogen-bonding interactions at the POT1-nucleic acid interface. At amino acid 62, Phe discriminates against RNA binding and Tyr allows RNA binding. We further show that TPP1 greatly augments POT1's discrimination against RNA.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309-0215, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protection of telomeres protein 1 A299Homo sapiensMutation(s): 0 
Gene Names: POT1
Find proteins for Q9NUX5 (Homo sapiens)
Explore Q9NUX5 
Go to UniProtKB:  Q9NUX5
NIH Common Fund Data Resources
PHAROS:  Q9NUX5
GTEx:  ENSG00000128513
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA/RNA (5'-D(*T)-R(P*U)-D(P*AP*GP*GP*GP*TP*TP*AP*G)-3')B10N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.80 Å
    • R-Value Free: 0.238 
    • R-Value Work: 0.228 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 101.867α = 90
    b = 103.591β = 90
    c = 71.736γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSrefinement
    PDB_EXTRACTdata extraction
    BOSdata collection
    HKL-2000data reduction
    HKL-2000data scaling
    REFMACphasing

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2010-01-19
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2017-11-01
      Changes: Refinement description