4TU7

Structure of U2AF65 D231V variant with BrU5 DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA.

Agrawal, A.A.McLaughlin, K.J.Jenkins, J.L.Kielkopf, C.L.

(2014) Proc Natl Acad Sci U S A 111: 17420-17425

  • DOI: 10.1073/pnas.1412743111
  • Primary Citation of Related Structures:  
    4TU7, 4TU8, 4TU9

  • PubMed Abstract: 
  • Purine interruptions of polypyrimidine (Py) tract splice site signals contribute to human genetic diseases. The essential splicing factor U2AF(65) normally recognizes a Py tract consensus sequence preceding the major class of 3' splice sites. We found that neurofibromatosis- or retinitis pigmentosa-causing mutations in the 5' regions of Py tracts severely reduce U2AF(65) affinity ...

    Purine interruptions of polypyrimidine (Py) tract splice site signals contribute to human genetic diseases. The essential splicing factor U2AF(65) normally recognizes a Py tract consensus sequence preceding the major class of 3' splice sites. We found that neurofibromatosis- or retinitis pigmentosa-causing mutations in the 5' regions of Py tracts severely reduce U2AF(65) affinity. Conversely, we identified a preferred binding site of U2AF(65) for purine substitutions in the 3' regions of Py tracts. Based on a comparison of new U2AF(65) structures bound to either A- or G-containing Py tracts with previously identified pyrimidine-containing structures, we expected to find that a D231V amino acid change in U2AF(65) would specify U over other nucleotides. We found that the crystal structure of the U2AF(65)-D231V variant confirms favorable packing between the engineered valine and a target uracil base. The D231V amino acid change restores U2AF(65) affinity for two mutated splice sites that cause human genetic diseases and successfully promotes splicing of a defective retinitis pigmentosa-causing transcript. We conclude that reduced U2AF(65) binding is a molecular consequence of disease-relevant mutations, and that a structure-guided U2AF(65) variant is capable of manipulating gene expression in eukaryotic cells.


    Organizational Affiliation

    Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642 clara_kielkopf@urmc.rochester.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor U2AF 65 kDa subunitA, B174Homo sapiensMutation(s): 1 
Gene Names: U2AF2U2AF65
UniProt & NIH Common Fund Data Resources
Find proteins for P26368 (Homo sapiens)
Explore P26368 
Go to UniProtKB:  P26368
PHAROS:  P26368
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*UP*UP*UP*UP*(BRU)P*UP*U)-3')D [auth E], C [auth P]7synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CPQ (Subject of Investigation/LOI)
    Query on CPQ

    Download Ideal Coordinates CCD File 
    O [auth B]N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
    C42 H75 N3 O15
    OJSUWTDDXLCUFR-HGZMBBKESA-N
     Ligand Interaction
    SO4
    Query on SO4

    Download Ideal Coordinates CCD File 
    G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B]SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    J [auth A], K [auth A], L [auth A], S [auth B]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    DIO
    Query on DIO

    Download Ideal Coordinates CCD File 
    E [auth A], F [auth A], M [auth B], N [auth B]1,4-DIETHYLENE DIOXIDE
    C4 H8 O2
    RYHBNJHYFVUHQT-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.09 Å
    • R-Value Free: 0.223 
    • R-Value Work: 0.174 
    • R-Value Observed: 0.179 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 164.432α = 90
    b = 37.361β = 125.6
    c = 100.192γ = 90
    Software Package:
    Software NamePurpose
    SCALAdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-11-26
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Database references
    • Version 1.2: 2014-12-24
      Changes: Database references
    • Version 1.3: 2017-11-22
      Changes: Database references, Derived calculations, Refinement description, Source and taxonomy