Crystal Structure of Human Prp8, Residues 1755-2016

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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Structure and function of an RNase H domain at the heart of the spliceosome.

Pena, V.Rozov, A.Fabrizio, P.Luhrmann, R.Wahl, M.C.

(2008) EMBO J 27: 2929-2940

  • DOI: https://doi.org/10.1038/emboj.2008.209
  • Primary Citation of Related Structures:  
    3E9L, 3E9O, 3E9P

  • PubMed Abstract: 

    Precursor-messenger RNA (pre-mRNA) splicing encompasses two sequential transesterification reactions in distinct active sites of the spliceosome that are transiently established by the interplay of small nuclear (sn) RNAs and spliceosomal proteins. Protein Prp8 is an active site component but the molecular mechanisms, by which it might facilitate splicing catalysis, are unknown. We have determined crystal structures of corresponding portions of yeast and human Prp8 that interact with functional regions of the pre-mRNA, revealing a phylogenetically conserved RNase H fold, augmented by Prp8-specific elements. Comparisons to RNase H-substrate complexes suggested how an RNA encompassing a 5'-splice site (SS) could bind relative to Prp8 residues, which on mutation, suppress splice defects in pre-mRNAs and snRNAs. A truncated RNase H-like active centre lies next to a known contact region of the 5'SS and directed mutagenesis confirmed that this centre is a functional hotspot. These data suggest that Prp8 employs an RNase H domain to help assemble and stabilize the spliceosomal catalytic core, coordinate the activities of other splicing factors and possibly participate in chemical catalysis of splicing.

  • Organizational Affiliation

    Abteilung Zelluläre Biochemie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8257Homo 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: 1.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.426α = 90
b = 83.426β = 90
c = 96.263γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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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, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations