4NUT

Crystal structure of the complex between Snu13p and the PEP domain of Rsa1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control

Bizarro, J., Charron, C., Boulon, S., Westman, B., Pradet-Balade, B., Vandermoere, F., Chagot, M.E., Hallais, M., Ahmad, Y., Leonhardt, H., Lamond, A., Manival, X., Branlant, C., Charpentier, B., Verheggen, C., Bertrand, E.

(2014) J Cell Biol 207: 463-480

  • DOI: 10.1083/jcb.201404160
  • Primary Citation of Related Structures:  
    4NUT

  • PubMed Abstract: 

    • In vitro, assembly of box C/D small nucleolar ribonucleoproteins (snoRNPs) involves the sequential recruitment of core proteins to snoRNAs. In vivo, however, assembly factors are required (NUFIP, BCD1, and the HSP90-R2TP complex), and it is unknown whether a similar sequential scheme applies ...

    In vitro, assembly of box C/D small nucleolar ribonucleoproteins (snoRNPs) involves the sequential recruitment of core proteins to snoRNAs. In vivo, however, assembly factors are required (NUFIP, BCD1, and the HSP90-R2TP complex), and it is unknown whether a similar sequential scheme applies. In this paper, we describe systematic quantitative stable isotope labeling by amino acids in cell culture proteomic experiments and the crystal structure of the core protein Snu13p/15.5K bound to a fragment of the assembly factor Rsa1p/NUFIP. This revealed several unexpected features: (a) the existence of a protein-only pre-snoRNP complex containing five assembly factors and two core proteins, 15.5K and Nop58; (b) the characterization of ZNHIT3, which is present in the protein-only complex but gets released upon binding to C/D snoRNAs; (c) the dynamics of the R2TP complex, which appears to load/unload RuvBL AAA(+) adenosine triphosphatase from pre-snoRNPs; and (d) a potential mechanism for preventing premature activation of snoRNP catalytic activity. These data provide a framework for understanding the assembly of box C/D snoRNPs.

    Organizational Affiliation: 

    Equipe labellisée Ligue contre le Cancer, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535, Institut de Génétique Moléculaire de Montpellier, 34293 Montpellier, Cedex 5, France celine.verheggen@igmm.cnrs.fr edouard.bertrand@igmm.cnrs.fr.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinA129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13, YEL026W
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39990 
Go to UniProtKB:  P39990
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome assembly 1 proteinB57Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSA1, YPL193W
Find proteins for Q08932 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08932 
Go to UniProtKB:  Q08932
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
 C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.732α = 90
b = 59.732β = 90
c = 92.549γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release