4YH8

Structure of yeast U2AF complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A novel 3' splice site recognition by the two zinc fingers in the U2AF small subunit.

Yoshida, H.Park, S.Y.Oda, T.Akiyoshi, T.Sato, M.Shirouzu, M.Tsuda, K.Kuwasako, K.Unzai, S.Muto, Y.Urano, T.Obayashi, E.

(2015) Genes Dev 29: 1649-1660

  • DOI: 10.1101/gad.267104.115
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The pre-mRNA splicing reaction of eukaryotic cells has to be carried out extremely accurately, as failure to recognize the splice sites correctly causes serious disease. The small subunit of the U2AF heterodimer is essential for the determination of ...

    The pre-mRNA splicing reaction of eukaryotic cells has to be carried out extremely accurately, as failure to recognize the splice sites correctly causes serious disease. The small subunit of the U2AF heterodimer is essential for the determination of 3' splice sites in pre-mRNA splicing, and several single-residue mutations of the U2AF small subunit cause severe disorders such as myelodysplastic syndromes. However, the mechanism of RNA recognition is poorly understood. Here we solved the crystal structure of the U2AF small subunit (U2AF23) from fission yeast, consisting of an RNA recognition motif (RRM) domain flanked by two conserved CCCH-type zinc fingers (ZFs). The two ZFs are positioned side by side on the β sheet of the RRM domain. Further mutational analysis revealed that the ZFs bind cooperatively to the target RNA sequence, but the RRM domain acts simply as a scaffold to organize the ZFs and does not itself contact the RNA directly. This completely novel and unexpected mode of RNA-binding mechanism by the U2AF small subunit sheds light on splicing errors caused by mutations of this highly conserved protein.


    Organizational Affiliation

    Department of Biochemistry, Shimane University School of Medicine, Izumo 693-8501, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Splicing factor U2AF 23 kDa subunit
A
216Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: SPAP8A3.06
Find proteins for Q09176 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q09176

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Splicing factor U2AF 59 kDa subunit
B
71Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp2mis11SPBC146.07
Find proteins for P36629 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P36629
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: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.616α = 90
b = 112.704β = 90
c = 57.198γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and TechnologyJapan20112006

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Data collection, Database references, Derived calculations