The carboxy-terminal domain of Erb1 is a seven-bladed beta-propeller that binds RNA.

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


The Carboxy-Terminal Domain of Erb1 Is a Seven-Bladed -Propeller that Binds RNA.

Wegrecki, M.Neira, J.L.Bravo, J.

(2015) PLoS One 10: e0123463-e0123463

  • DOI: https://doi.org/10.1371/journal.pone.0123463
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Erb1 (Eukaryotic Ribosome Biogenesis 1) protein is essential for the maturation of the ribosomal 60S subunit. Functional studies in yeast and mammalian cells showed that altogether with Nop7 and Ytm1 it forms a stable subcomplex called PeBoW that is crucial for a correct rRNA processing. The exact function of the protein within the process remains unknown. The N-terminal region of the protein includes a well conserved region shown to be involved in PeBoW complex formation whereas the carboxy-terminal half was predicted to contain seven WD40 repeats. This first structural report on Erb1 from yeast describes the architecture of a seven-bladed β-propeller domain that revealed a characteristic extra motif formed by two α-helices and a β-strand that insert within the second WD repeat. We performed analysis of molecular surface and crystal packing, together with multiple sequence alignment and comparison of the structure with other β-propellers, in order to identify areas that are more likely to mediate protein-protein interactions. The abundance of many positively charged residues on the surface of the domain led us to investigate whether the propeller of Erb1 might be involved in RNA binding. Three independent assays confirmed that the protein interacted in vitro with polyuridilic acid (polyU), thus suggesting a possible role of the domain in rRNA rearrangement during ribosome biogenesis.

  • Organizational Affiliation

    Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche (Alicante), Spain; Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), 50009 Zaragoza, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ERB1826Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ERB1YMR049CYM9796.02C
Find proteins for Q04660 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04660 
Go to UniProtKB:  Q04660
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04660
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.024α = 90
b = 62.431β = 90
c = 158.218γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description