6G70

Structure of murine Prpf39


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1093/nar/gkz243
  • Primary Citation of Related Structures:  
    6G70

  • 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 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

    Institut für Chemie und Biochemie, RNA Biochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 39
A, B
670Mus musculusMutation(s): 0 
Gene Names: Prpf39
UniProt & NIH Common Fund Data Resources
Find proteins for Q8K2Z2 (Mus musculus)
Explore Q8K2Z2 
Go to UniProtKB:  Q8K2Z2
IMPC:  MGI:104602
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K2Z2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.49α = 90
b = 72.76β = 112.46
c = 207.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.2: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.3: 2020-04-22
    Changes: Database references
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references