The yeast ribosome synthesis factor Emg1 alpha beta knot fold methyltransferase

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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This is version 1.2 of the entry. See complete history


The Yeast Ribosome Synthesis Factor Emg1 is a Novel Member of the Superfamily of Alpha/Beta Knot Fold Methyltransferases.

Leulliot, N.Bohnsack, M.T.Graille, M.Tollervey, D.Van Tilbeurgh, H.

(2008) Nucleic Acids Res 36: 629

  • DOI: https://doi.org/10.1093/nar/gkm1074
  • Primary Citation of Related Structures:  
    2V3J, 2V3K

  • PubMed Abstract: 

    Emg1 was previously shown to be required for maturation of the 18S rRNA and biogenesis of the 40S ribosomal subunit. Here we report the determination of the crystal structure of Emg1 at 2 A resolution in complex with the methyl donor, S-adenosyl-methionine (SAM). This structure identifies Emg1 as a novel member of the alpha/beta knot fold methyltransferase (SPOUT) superfamily. In addition to the conserved SPOUT core, Emg1 has two unique domains that form an extended surface, which we predict to be involved in binding of RNA substrates. A point mutation within a basic patch on this surface almost completely abolished RNA binding in vitro. Three point mutations designed to disrupt the interaction of Emg1 with SAM each caused>100-fold reduction in SAM binding in vitro. Expression of only Emg1 with these mutations could support growth and apparently normal ribosome biogenesis in strains genetically depleted of Emg1. We conclude that the catalytic activity of Emg1 is not essential and that the presence of the protein is both necessary and sufficient for ribosome biogenesis.

  • Organizational Affiliation

    Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Bât 430, Université de Paris-Sud, 91405 Orsay Cedex, France. nicolas.leulliot@u-psud.fr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ESSENTIAL FOR MITOTIC GROWTH 1258Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06287 
Go to UniProtKB:  Q06287
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06287
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.479α = 90
b = 76.614β = 90
c = 87.561γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance