Crystal structure of the Rio2 kinase-ADP/Mg2+-phosphoaspartate complex from Chaetomium thermophilum

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.174 

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ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit.

Ferreira-Cerca, S.Sagar, V.Schafer, T.Diop, M.Wesseling, A.M.Lu, H.Chai, E.Hurt, E.Laronde-Leblanc, N.

(2012) Nat Struct Mol Biol 19: 1316-1323

  • DOI: https://doi.org/10.1038/nsmb.2403
  • Primary Citation of Related Structures:  
    4GYG, 4GYI

  • PubMed Abstract: 

    Ribosome synthesis involves dynamic association of ribosome-biogenesis factors with evolving preribosomal particles. Rio2 is an atypical protein kinase required for pre-40S subunit maturation. We report the crystal structure of eukaryotic Rio2-ATP-Mg(2+) complex. The active site contains ADP-Mg(2+) and a phosphoaspartate intermediate typically found in Na(+), K(+) and Ca(2+) ATPases but not protein kinases. Consistent with this finding, ctRio2 exhibits a robust ATPase activity in vitro. In vivo, Rio2 docks on the ribosome, with its active site occluded and its flexible loop positioned to interact with the pre-40S subunit. Moreover, Rio2 catalytic activity is required for its dissociation from the ribosome, a necessary step in pre-40S maturation. We propose that phosphoryl transfer from ATP to Asp257 in Rio2's active site and subsequent hydrolysis of the aspartylphosphate could be a trigger to power late cytoplasmic 40S subunit biogenesis.

  • Organizational Affiliation

    Biochemistry Center, University of Heidelberg, Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rio2 kinase397Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0033330Rio2
Find proteins for G0S5R3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S5R3 
Go to UniProtKB:  G0S5R3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S5R3
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.174 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.624α = 90
b = 119.624β = 90
c = 71.783γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Database references
  • Version 1.2: 2012-12-26
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description