Structural comparison of Yeast snoRNP and splicesomal protein snu13p with its homologs

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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This is version 1.4 of the entry. See complete history


Structural comparison of yeast snoRNP and spliceosomal protein Snu13p with its homologs

Oruganti, S.Zhang, Y.Li, H.

(2005) Biochem Biophys Res Commun 333: 550-554

  • DOI: https://doi.org/10.1016/j.bbrc.2005.05.141
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Snu13p is a bifunctional yeast protein involved in both messenger RNA splicing as well as ribosomal RNA maturation. Snu13p initiates assembly of ribonucleoprotein particles by interacting with a conserved RNA motif called kink turn. Unlike its archaeal homolog, L7Ae, Snu13p displays differential specificity for functionally distinct kink turns. Thus, the structures of Snu13p at different functional states, including those alone and bound with RNAs, are required to understand how the protein differentially interacts with kink turns. Although the structure of the human homolog of Snu13p bound with a spliceosomal RNA is known, there has not been a report of a structure of free Snu13p. This has hindered our ability to understand the structural basis for Snu13p's substrate specificity. We report a crystal structure of free Snu13p at 1.9A and a detailed structural comparison with its homologs. We show that free Snu13p has nearly an identical conformation as that of its human homolog bound with RNA. Interestingly, both eukaryotic proteins exhibit notable structural differences in their central beta-sheets as compared to their archaeal homolog, L7Ae. The observed structural differences offer a possible explanation to the observed difference in RNA specificity between Snu13p and L7Ae.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
126Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39990 
Go to UniProtKB:  P39990
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39990
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.133α = 90
b = 70.133β = 90
c = 54.701γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references