Crystal structure of the C-terminal domain of C. elegans pre-mRNA splicing factor Prp8 carrying R2303K mutant

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.230 

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Crystal structure of the C-terminal domain of splicing factor Prp8 carrying retinitis pigmentosa mutants

Zhang, L.Shen, J.Guarnieri, M.T.Heroux, A.Yang, K.Zhao, R.

(2007) Protein Sci 16: 1024-1031

  • DOI: https://doi.org/10.1110/ps.072872007
  • Primary Citation of Related Structures:  
    2P87, 2P8R

  • PubMed Abstract: 

    Prp8 is a critical pre-mRNA splicing factor. Prp8 is proposed to help form and stabilize the spliceosome catalytic core and to be an important regulator of spliceosome activation. Mutations in human Prp8 (hPrp8) cause a severe form of the genetic disorder retinitis pigmentosa, RP13. Understanding the molecular mechanism of Prp8's function in pre-mRNA splicing and RP13 has been hindered by its large size (over 2000 amino acids) and remarkably low-sequence similarity with other proteins. Here we present the crystal structure of the C-terminal domain (the last 273 residues) of Caenorhabditis elegans Prp8 (cPrp8). The core of the C-terminal domain is an alpha/beta structure that forms the MPN (Mpr1, Pad1 N-terminal) fold but without Zn(2+) coordination. We propose that the C-terminal domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. Mapping of RP13 mutants on the Prp8 structure suggests that these residues constitute a binding surface between Prp8 and other partner(s), and the disruption of this interaction provides a plausible molecular mechanism for RP13.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor Prp8273Caenorhabditis elegansMutation(s): 1 
Gene Names: prp-8
Find proteins for P34369 (Caenorhabditis elegans)
Explore P34369 
Go to UniProtKB:  P34369
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34369
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.225α = 90
b = 65.225β = 90
c = 136.437γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2007-09-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-08-31
    Changes: Structure summary
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references