Crystal Structure of PRP8 core domain IV

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural elucidation of a PRP8 core domain from the heart of the spliceosome.

Ritchie, D.B.Schellenberg, M.J.Gesner, E.M.Raithatha, S.A.Stuart, D.T.Macmillan, A.M.

(2008) Nat Struct Mol Biol 15: 1199-1205

  • DOI: https://doi.org/10.1038/nsmb.1505
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The spliceosome is a complex ribonucleoprotein (RNP) particle containing five RNAs and more than 100 associated proteins. One of these proteins, PRP8, has been shown to interact directly with the splice sites and branch region of precursor-mRNAs (pre-mRNAs) and spliceosomal RNAs associated with catalysis of the two steps of splicing. The 1.85-A X-ray structure of the core of PRP8 domain IV, implicated in key spliceosomal interactions, reveals a bipartite structure that includes the presence of an RNase H fold linked to a five-helix assembly. Analysis of mutant yeast alleles and cross-linking results in the context of this structure, coupled with RNA binding studies, suggests that domain IV forms a surface that interacts directly with the RNA structures at the catalytic core of the spliceosome.

  • Organizational Affiliation

    Department of Biochemistry, 474 Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G2H7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8
A, B
222Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P2Q9 (Homo sapiens)
Explore Q6P2Q9 
Go to UniProtKB:  Q6P2Q9
GTEx:  ENSG00000174231 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P2Q9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.397α = 90
b = 78.062β = 90
c = 93.575γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references