The structure of XendoU: a splicing independent snoRNA processing endoribonuclease

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.274 

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The Structure of the Endoribonuclease Xendou: From Small Nucleolar RNA Processing to Severe Acute Respiratory Syndrome Coronavirus Replication.

Renzi, F.Caffarelli, E.Laneve, P.Bozzoni, I.Brunori, M.Vallone, B.

(2006) Proc Natl Acad Sci U S A 103: 12365

  • DOI: https://doi.org/10.1073/pnas.0602426103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Small nucleolar RNAs (snoRNAs) play a key role in eukaryotic ribosome biogenesis. In most cases, snoRNAs are encoded in introns and are released through the splicing reaction. Some snoRNAs are, instead, produced by an alternative pathway consisting of endonucleolytic processing of pre-mRNA. XendoU, the endoribonuclease responsible for this activity, is a U-specific, metal-dependent enzyme that releases products with 2'-3' cyclic phosphate termini. XendoU is broadly conserved among eukaryotes, and it is a genetic marker of nidoviruses, including the severe acute respiratory syndrome coronavirus, where it is essential for replication and transcription. We have determined by crystallography the structure of XendoU that, by refined search methodologies, appears to display a unique fold. Based on sequence conservation, mutagenesis, and docking simulations, we have identified the active site. The conserved structural determinants of this site may provide a framework for attempting to design antiviral drugs to interfere with the infectious nidovirus life cycle.

  • Organizational Affiliation

    Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, 00185 Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
292Xenopus laevisMutation(s): 0 
Find proteins for Q8JFY9 (Xenopus laevis)
Explore Q8JFY9 
Go to UniProtKB:  Q8JFY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JFY9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.274 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.451α = 90
b = 53.204β = 121.86
c = 133.466γ = 90
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: 2006-07-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other