Crystal Structure of the Mouse Dom3Z

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1.

Xiang, S.Cooper-Morgan, A.Jiao, X.Kiledjian, M.Manley, J.L.Tong, L.

(2009) Nature 458: 784-788

  • DOI: https://doi.org/10.1038/nature07731
  • Primary Citation of Related Structures:  
    3FQD, 3FQG, 3FQI, 3FQJ

  • PubMed Abstract: 

    The 5'-->3' exoribonucleases (XRNs) comprise a large family of conserved enzymes in eukaryotes with crucial functions in RNA metabolism and RNA interference. XRN2, or Rat1 in yeast, functions primarily in the nucleus and also has an important role in transcription termination by RNA polymerase II (refs 7-14). Rat1 exoribonuclease activity is stimulated by the protein Rai1 (refs 15, 16). Here we report the crystal structure at 2.2 A resolution of Schizosaccharomyces pombe Rat1 in complex with Rai1, as well as the structures of Rai1 and its murine homologue Dom3Z alone at 2.0 A resolution. The structures reveal the molecular mechanism for the activation of Rat1 by Rai1 and for the exclusive exoribonuclease activity of Rat1. Biochemical studies confirm these observations, and show that Rai1 allows Rat1 to degrade RNAs with stable secondary structure more effectively. There are large differences in the active site landscape of Rat1 compared to related and PIN (PilT N terminus) domain-containing nucleases. Unexpectedly, we identified a large pocket in Rai1 and Dom3Z that contains highly conserved residues, including three acidic side chains that coordinate a divalent cation. Mutagenesis and biochemical studies demonstrate that Rai1 possesses pyrophosphohydrolase activity towards 5' triphosphorylated RNA. Such an activity is important for messenger RNA degradation in bacteria, but this is, to our knowledge, the first demonstration of this activity in eukaryotes and suggests that Rai1/Dom3Z may have additional important functions in RNA metabolism.

  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Dom3Z417Mus musculusMutation(s): 0 
Gene Names: Dom3zNg6
Find proteins for O70348 (Mus musculus)
Explore O70348 
Go to UniProtKB:  O70348
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO70348
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EPE

Download Ideal Coordinates CCD File 
C8 H18 N2 O4 S
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.979α = 90
b = 88.379β = 114.2
c = 50.069γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations