1H64

CRYSTAL STRUCTURE OF THE SM-RELATED PROTEIN OF P. ABYSSI: THE BIOLOGICAL UNIT IS A HEPTAMER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of the Pyrococcus Abyssi Sm Core and its Complex with RNA.Common Features of RNA Binding in Archaea and Eukarya

Thore, S.Mayer, C.Sauter, C.Weeks, S.Suck, D.

(2003) J Biol Chem 278: 1239

  • DOI: https://doi.org/10.1074/jbc.M207685200
  • Primary Citation of Related Structures:  
    1H64, 1M8V

  • PubMed Abstract: 

    The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. Their proposed function is to mediate RNA-RNA interactions. We present here the crystal structures of Pyrococcus abyssi Sm protein (PA-Sm1) and its complex with a uridine heptamer. The overall structure of the protein complex, a heptameric ring with a central cavity, is similar to that proposed for the eukaryotic Sm core complex and found for other archaeal Sm proteins. RNA molecules bind to the protein at two different sites. They interact specifically inside the ring with three highly conserved residues, defining the uridine-binding pocket. In addition, nucleotides also interact on the surface formed by the N-terminal alpha-helix as well as a conserved aromatic residue in beta-strand 2 of the PA-Sm1 protein. The mutation of this conserved aromatic residue shows the importance of this second site for the discrimination between RNA sequences. Given the high structural homology between archaeal and eukaryotic Sm proteins, the PA-Sm1.RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions.


  • Organizational Affiliation

    Structural Biology Program, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SNRNP SM-LIKE PROTEIN75Pyrococcus abyssiMutation(s): 0 
UniProt
Find proteins for Q9V0Y8 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V0Y8 
Go to UniProtKB:  Q9V0Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V0Y8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.33α = 90.21
b = 70.16β = 97.7
c = 116.01γ = 107.48
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance