4BSZ

Crystal Structure of the Yeast Ribosomal Protein Rps3 in Complex with its Chaperone Yar1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of the Yeast Ribosomal Protein Rps3 in Complex with its Chaperone Yar1

Holzer, S.Ban, N.Klinge, S.

(2013) J Mol Biol 425: 4154

  • DOI: https://doi.org/10.1016/j.jmb.2013.08.022
  • Primary Citation of Related Structures:  
    4BSZ

  • PubMed Abstract: 

    Eukaryotic ribosome assembly involves a plethora of factors, which ensure that a correctly folded ribosome contains all ribosomal protein components. Among these assembly factors, Yar1 has recently emerged as a molecular chaperone for ribosomal protein rpS3 of the small ribosomal subunit (40S) in yeast. In complex with its chaperone, rpS3 is imported into the nucleus and protected from aggregation. How rpS3 and other ribosomal proteins are initially sequestered and subsequently integrated into pre-ribosomal particles is currently poorly understood. Here, we present the crystal structure of yeast rpS3 in complex with its chaperone Yar1 at 2.8Å resolution. The crystal structure rationalizes how Yar1 can protect rpS3 from aggregation while facilitating nuclear import and suggests a mechanism for a stepwise exchange of molecular partners that ribosomal proteins interact with during ribosome assembly.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Department of Biology, Eidgenössische Technische Hochschule Zürich, Schafmattstrasse 20, 8093 Zurich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S3244Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05750 
Go to UniProtKB:  P05750
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05750
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ANKYRIN REPEAT-CONTAINING PROTEIN YAR1202Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
Find proteins for P46683 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46683 
Go to UniProtKB:  P46683
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46683
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.83α = 90
b = 104.83β = 90
c = 95.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Structure summary
  • Version 1.2: 2013-09-25
    Changes: Database references
  • Version 1.3: 2013-11-13
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description