7KJT

KEOPS tRNA modifying sub-complex of archaeal Cgi121 and tRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A substrate binding model for the KEOPS tRNA modifying complex.

Beenstock, J.Ona, S.M.Porat, J.Orlicky, S.Wan, L.C.K.Ceccarelli, D.F.Maisonneuve, P.Szilard, R.K.Yin, Z.Setiaputra, D.Mao, D.Y.L.Khan, M.Raval, S.Schriemer, D.C.Bayfield, M.A.Durocher, D.Sicheri, F.

(2020) Nat Commun 11: 6233-6233

  • DOI: 10.1038/s41467-020-19990-5
  • Primary Citation of Related Structures:  
    7KJT, 7KJU

  • PubMed Abstract: 
  • The KEOPS complex, which is conserved across archaea and eukaryotes, is composed of four core subunits; Pcc1, Kae1, Bud32 and Cgi121. KEOPS is crucial for the fitness of all organisms examined. In humans, pathogenic mutations in KEOPS genes lead to G ...

    The KEOPS complex, which is conserved across archaea and eukaryotes, is composed of four core subunits; Pcc1, Kae1, Bud32 and Cgi121. KEOPS is crucial for the fitness of all organisms examined. In humans, pathogenic mutations in KEOPS genes lead to Galloway-Mowat syndrome, an autosomal-recessive disease causing childhood lethality. Kae1 catalyzes the universal and essential tRNA modification N 6 -threonylcarbamoyl adenosine, but the precise roles of all other KEOPS subunits remain an enigma. Here we show using structure-guided studies that Cgi121 recruits tRNA to KEOPS by binding to its 3' CCA tail. A composite model of KEOPS bound to tRNA reveals that all KEOPS subunits form an extended tRNA-binding surface that we have validated in vitro and in vivo to mediate the interaction with the tRNA substrate and its modification. These findings provide a framework for understanding the inner workings of KEOPS and delineate why all KEOPS subunits are essential.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, ON, Canada. sicheri@lunenfeld.ca.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Regulatory protein Cgi121H150Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: cgi121MJ0187
Find proteins for Q57646 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57646 
Go to UniProtKB:  Q57646
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (70-MER)A76Methanocaldococcus jannaschii
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.284α = 90
b = 121.284β = 90
c = 91.734γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaFDN 143277

Revision History 

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references