6G70

Structure of murine Prpf39


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Increased versatility despite reduced molecular complexity: evolution, structure and function of metazoan splicing factor PRPF39.

De Bortoli, F.Neumann, A.Kotte, A.Timmermann, B.Schuler, T.Wahl, M.C.Loll, B.Heyd, F.

(2019) Nucleic Acids Res. 47: 5867-5879

  • DOI: 10.1093/nar/gkz243

  • PubMed Abstract: 
  • In the yeast U1 snRNP the Prp39/Prp42 heterodimer is essential for early steps of spliceosome assembly. In metazoans no Prp42 ortholog exists, raising the question how the heterodimer is functionally substituted. Here we present the crystal structure ...

    In the yeast U1 snRNP the Prp39/Prp42 heterodimer is essential for early steps of spliceosome assembly. In metazoans no Prp42 ortholog exists, raising the question how the heterodimer is functionally substituted. Here we present the crystal structure of murine PRPF39, which forms a homodimer. Structure-guided point mutations disrupt dimer formation and inhibit splicing, manifesting the homodimer as functional unit. PRPF39 expression is controlled by NMD-inducing alternative splicing in mice and human, suggesting a role in adapting splicing efficiency to cell type specific requirements. A phylogenetic analysis reveals coevolution of shortened U1 snRNA and the absence of Prp42, which correlates with overall splicing complexity in different fungi. While current models correlate the diversity of spliceosomal proteins with splicing complexity, our study highlights a contrary case. We find that organisms with higher splicing complexity have substituted the Prp39/Prp42 heterodimer with a PRPF39 homodimer.


    Organizational Affiliation

    Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Ihnestraße 63-73, Berlin 14195, Germany.,Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, 39120 Magdeburg, Germany.,Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany.,Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 39
A, B
670Mus musculusMutation(s): 0 
Gene Names: Prpf39
Find proteins for Q8K2Z2 (Mus musculus)
Go to UniProtKB:  Q8K2Z2
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 189.490α = 90.00
b = 72.760β = 112.46
c = 207.100γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Advisory, Data collection, Database references, Derived calculations
  • Version 1.2: 2019-06-26
    Type: Data collection, Database references