3G9Y

Crystal structure of the second zinc finger from ZRANB2/ZNF265 bound to 6 nt ssRNA sequence AGGUAA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences

Loughlin, F.E.Mansfield, R.E.Vaz, P.M.McGrath, A.P.Setiyaputra, S.Gamsjaeger, R.Chen, E.S.Morris, B.J.Guss, J.M.Mackay, J.P.

(2009) Proc Natl Acad Sci U S A 106: 5581-5586

  • DOI: 10.1073/pnas.0802466106
  • Primary Citation of Related Structures:  
    3G9Y

  • PubMed Abstract: 
  • The alternative splicing of mRNA is a critical process in higher eukaryotes that generates substantial proteomic diversity. Many of the proteins that are essential to this process contain arginine/serine-rich (RS) domains. ZRANB2 is a widely-expresse ...

    The alternative splicing of mRNA is a critical process in higher eukaryotes that generates substantial proteomic diversity. Many of the proteins that are essential to this process contain arginine/serine-rich (RS) domains. ZRANB2 is a widely-expressed and highly-conserved RS-domain protein that can regulate alternative splicing but lacks canonical RNA-binding domains. Instead, it contains 2 RanBP2-type zinc finger (ZnF) domains. We demonstrate that these ZnFs recognize ssRNA with high affinity and specificity. Each ZnF binds to a single AGGUAA motif and the 2 domains combine to recognize AGGUAA(N(x))AGGUAA double sites, suggesting that ZRANB2 regulates alternative splicing via a direct interaction with pre-mRNA at sites that resemble the consensus 5' splice site. We show using X-ray crystallography that recognition of an AGGUAA motif by a single ZnF is dominated by side-chain hydrogen bonds to the bases and formation of a guanine-tryptophan-guanine "ladder." A number of other human proteins that function in RNA processing also contain RanBP2 ZnFs in which the RNA-binding residues of ZRANB2 are conserved. The ZnFs of ZRANB2 therefore define another class of RNA-binding domain, advancing our understanding of RNA recognition and emphasizing the versatility of ZnF domains in molecular recognition.


    Related Citations: 
    • Crystallization of a ZRANB2-RNA complex
      Loughlin, F.E., Lee, M., Guss, J.M., Mackay, J.P.
      (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 1175

    Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, Sydney NSW 2006, Australia.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger Ran-binding domain-containing protein 2A33Homo sapiensMutation(s): 0 
Gene Names: ZRANB2ZISZNF265
Find proteins for O95218 (Homo sapiens)
Explore O95218 
Go to UniProtKB:  O95218
NIH Common Fund Data Resources
PHAROS  O95218
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*GP*GP*UP*AP*A)-3')C6N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    A
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.40 Å
    • R-Value Free: 0.235 
    • R-Value Work: 0.201 
    • R-Value Observed: 0.203 
    • Space Group: P 65 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 54.519α = 90
    b = 54.519β = 90
    c = 48.071γ = 120
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data collection
    HKL-2000data reduction
    HKL-2000data scaling
    SHELXEmodel building
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2009-03-03
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Advisory, Version format compliance
    • Version 1.2: 2017-11-01
      Changes: Refinement description