5A53

Crystal Structure of the Rpf2-Rrs1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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This is version 1.1 of the entry. See complete history


Literature

Chaperoning 5S RNA Assembly.

Madru, C.Lebaron, S.Blaud, M.Delbos, L.Pipoli, J.Pasmant, E.Rety, S.Leulliot, N.

(2015) Genes Dev 29: 1432

  • DOI: https://doi.org/10.1101/gad.260349.115
  • Primary Citation of Related Structures:  
    5A53

  • PubMed Abstract: 

    In eukaryotes, three of the four ribosomal RNAs (rRNAs)—the 5.8S, 18S, and 25S/28S rRNAs—are processed from a single pre-rRNA transcript and assembled into ribosomes. The fourth rRNA, the 5S rRNA, is transcribed by RNA polymerase III and is assembled into the 5S ribonucleoprotein particle (RNP), containing ribosomal proteins Rpl5/uL18 and Rpl11/uL5, prior to its incorporation into preribosomes. In mammals, the 5S RNP is also a central regulator of the homeostasis of the tumor suppressor p53. The nucleolar localization of the 5S RNP and its assembly into preribosomes are performed by a specialized complex composed of Rpf2 and Rrs1 in yeast or Bxdc1 and hRrs1 in humans. Here we report the structural and functional characterization of the Rpf2-Rrs1 complex alone, in complex with the 5S RNA, and within pre-60S ribosomes. We show that the Rpf2-Rrs1 complex contains a specialized 5S RNA E-loop-binding module, contacts the Rpl5 protein, and also contacts the ribosome assembly factor Rsa4 and the 25S RNA. We propose that the Rpf2-Rrs1 complex establishes a network of interactions that guide the incorporation of the 5S RNP in preribosomes in the initial conformation prior to its rotation to form the central protuberance found in the mature large ribosomal subunit.


  • Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques, UMR, CNRS 8015, Université Paris Descartes, Faculté de Pharmacie, Sorbonne Paris Cité, 75006 Paris, France;


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
REGULATOR OF RIBOSOME BIOSYNTHESIS65Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q08746 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08746 
Go to UniProtKB:  Q08746
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08746
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
REGULATOR OF RIBOSOME BIOSYNTHESIS22Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q08746 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08746 
Go to UniProtKB:  Q08746
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08746
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOME BIOGENESIS PROTEIN RPF2230Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36160 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36160 
Go to UniProtKB:  P36160
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36160
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.28α = 90
b = 72.28β = 90
c = 175.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other