4M5D

Crystal structure of the Utp22 and Rrp7 complex from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme.

Lin, J.Lu, J.Feng, Y.Sun, M.Ye, K.

(2013) PLoS Biol 11: e1001669-e1001669

  • DOI: 10.1371/journal.pbio.1001669
  • Primary Citation of Related Structures:  
    2MBY, 4M5D

  • PubMed Abstract: 
  • A multitude of proteins and small nucleolar RNAs transiently associate with eukaryotic ribosomal RNAs to direct their modification and processing and the assembly of ribosomal proteins. Utp22 and Rrp7, two interacting proteins with no recognizable domain, are components of the 90S preribosome or the small subunit processome that conducts early processing of 18S rRNA ...

    A multitude of proteins and small nucleolar RNAs transiently associate with eukaryotic ribosomal RNAs to direct their modification and processing and the assembly of ribosomal proteins. Utp22 and Rrp7, two interacting proteins with no recognizable domain, are components of the 90S preribosome or the small subunit processome that conducts early processing of 18S rRNA. Here, we determine the cocrystal structure of Utp22 and Rrp7 complex at 1.97 Å resolution and the NMR structure of a C-terminal fragment of Rrp7, which is not visible in the crystal structure. The structure reveals that Utp22 surprisingly resembles a dimeric class I tRNA CCA-adding enzyme yet with degenerate active sites, raising an interesting evolutionary connection between tRNA and rRNA processing machineries. Rrp7 binds extensively to Utp22 using a deviant RNA recognition motif and an extended linker. Functional sites on the two proteins were identified by structure-based mutagenesis in yeast. We show that Rrp7 contains a flexible RNA-binding C-terminal tail that is essential for association with preribosomes. RNA-protein crosslinking shows that Rrp7 binds at the central domain of 18S rRNA and shares a neighborhood with two processing H/ACA snoRNAs snR30 and snR10. Depletion of snR30 prevents the stable assembly of Rrp7 into preribosomes. Our results provide insight into the evolutionary origin and functional context of Utp22 and Rrp7.


    Organizational Affiliation

    National Institute of Biological Sciences, Beijing, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 22 A1237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22YGR090W
Find proteins for P53254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53254 
Go to UniProtKB:  P53254
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 7 B297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7YCL031CYCL184YCL31C
Find proteins for P25368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25368 
Go to UniProtKB:  P25368
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.257α = 90
b = 129.56β = 90
c = 214.44γ = 90
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-08-08 
  • Released Date: 2013-11-06 
  • Deposition Author(s): Lin, J., Ye, K.

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release