7C07

Crystal structure of yeast U2AF1 complex bound to 5'-AAGGU RNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1.

Yoshida, H.Park, S.Y.Sakashita, G.Nariai, Y.Kuwasako, K.Muto, Y.Urano, T.Obayashi, E.

(2020) Nat Commun 11: 4744-4744

  • DOI: 10.1038/s41467-020-18559-6
  • Primary Citation of Related Structures:  
    7C06, 7C07, 7C08

  • PubMed Abstract: 
  • The accurate exclusion of introns by RNA splicing is critical for the production of mature mRNA. U2AF1 binds specifically to the 3´ splice site, which includes an essential AG dinucleotide. Even a single amino acid mutation of U2AF1 can cause serious ...

    The accurate exclusion of introns by RNA splicing is critical for the production of mature mRNA. U2AF1 binds specifically to the 3´ splice site, which includes an essential AG dinucleotide. Even a single amino acid mutation of U2AF1 can cause serious disease such as certain cancers or myelodysplastic syndromes. Here, we describe the first crystal structures of wild-type and pathogenic mutant U2AF1 complexed with target RNA, revealing the mechanism of 3´ splice site selection, and how aberrant splicing results from clinically important mutations. Unexpected features of this mechanism may assist the future development of new treatments against diseases caused by splicing errors.


    Organizational Affiliation

    Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, 693-8501, Japan. eijioba@med.shimane-u.ac.jp.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor U2AF 23 kDa subunitADGJMPSVY216Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: SPAP8A3.06
Find proteins for Q09176 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q09176 
Go to UniProtKB:  Q09176
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor U2AF 59 kDa subunitBEHKNQTWZ69Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: prp2mis11SPBC146.07
Find proteins for P36629 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P36629 
Go to UniProtKB:  P36629
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*U*AP*AP*GP*GP*U)-3')1, C, F, I, L, O, R, U, X6synthetic construct
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    A, D, G, J, M, P, S, V, Y
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.20 Å
    • R-Value Free: 0.285 
    • R-Value Work: 0.255 
    • R-Value Observed: 0.256 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 94.487α = 90
    b = 256.947β = 100.751
    c = 94.591γ = 90
    Software Package:
    Software NamePurpose
    XDSdata reduction
    Aimlessdata scaling
    MOLREPphasing
    PHENIXrefinement

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Japan Society for the Promotion of Science (JSPS)Japan18K06086

    Revision History 

    • Version 1.0: 2020-09-30
      Type: Initial release
    • Version 1.1: 2020-10-07
      Changes: Database references