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: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 

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.USA 106: 5581-5586

  • DOI: 10.1073/pnas.0802466106

  • 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 64: 1175


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc finger Ran-binding domain-containing protein 2
A
33Homo sapiensMutation(s): 0 
Gene Names: ZRANB2 (ZIS, ZNF265)
Find proteins for O95218 (Homo sapiens)
Go to Gene View: ZRANB2
Go to UniProtKB:  O95218
Entity ID: 2
MoleculeChainsLengthOrganism
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 SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 54.519α = 90.00
b = 54.519β = 90.00
c = 48.071γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
SHELXEmodel building
HKL-2000data collection
DENZOdata reduction
REFMACrefinement
PHASERphasing
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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