3VAK

Structure of U2AF65 variant with BrU5 DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.

Jenkins, J.L.Agrawal, A.A.Gupta, A.Green, M.R.Kielkopf, C.L.

(2013) Nucleic Acids Res 41: 3859-3873

  • DOI: 10.1093/nar/gkt046
  • Primary Citation of Related Structures:  
    3VAF, 3VAG, 3VAH, 3VAI, 3VAJ, 3VAK, 3VAL, 3VAM

  • PubMed Abstract: 
  • Degenerate splice site sequences mark the intron boundaries of pre-mRNA transcripts in multicellular eukaryotes. The essential pre-mRNA splicing factor U2AF(65) is faced with the paradoxical tasks of accurately targeting polypyrimidine (Py) tracts pr ...

    Degenerate splice site sequences mark the intron boundaries of pre-mRNA transcripts in multicellular eukaryotes. The essential pre-mRNA splicing factor U2AF(65) is faced with the paradoxical tasks of accurately targeting polypyrimidine (Py) tracts preceding 3' splice sites while adapting to both cytidine and uridine nucleotides with nearly equivalent frequencies. To understand how U2AF(65) recognizes degenerate Py tracts, we determined six crystal structures of human U2AF(65) bound to cytidine-containing Py tracts. As deoxy-ribose backbones were required for co-crystallization with these Py tracts, we also determined two baseline structures of U2AF(65) bound to the deoxy-uridine counterparts and compared the original, RNA-bound structure. Local structural changes suggest that the N-terminal RNA recognition motif 1 (RRM1) is more promiscuous for cytosine-containing Py tracts than the C-terminal RRM2. These structural differences between the RRMs were reinforced by the specificities of wild-type and site-directed mutant U2AF(65) for region-dependent cytosine- and uracil-containing RNA sites. Small-angle X-ray scattering analyses further demonstrated that Py tract variations select distinct inter-RRM spacings from a pre-existing ensemble of U2AF(65) conformations. Our results highlight both local and global conformational selection as a means for universal 3' splice site recognition by U2AF(65).


    Organizational Affiliation

    Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor U2AF 65 kDa subunitAB174Homo sapiensMutation(s): 0 
Gene Names: U2AF2U2AF65
Find proteins for P26368 (Homo sapiens)
Explore P26368 
Go to UniProtKB:  P26368
NIH Common Fund Data Resources
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')E, P7synthetic construct
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CPQ
    Query on CPQ

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

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    A, B
    SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    GOL
    Query on GOL

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    A, B
    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    DIO
    Query on DIO

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    A, B
    1,4-DIETHYLENE DIOXIDE
    C4 H8 O2
    RYHBNJHYFVUHQT-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.17 Å
    • R-Value Free: 0.229 
    • R-Value Work: 0.188 
    • R-Value Observed: 0.192 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 166.406α = 90
    b = 37.726β = 125.43
    c = 101.631γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data collection

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2013-02-13
      Type: Initial release
    • Version 1.1: 2013-05-22
      Changes: Database references
    • Version 1.2: 2017-08-16
      Changes: Refinement description, Source and taxonomy