6GWJ

Human OSGEP / LAGE3 / GON7 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Defects in t 6 A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.

Arrondel, C.Missoury, S.Snoek, R.Patat, J.Menara, G.Collinet, B.Liger, D.Durand, D.Gribouval, O.Boyer, O.Buscara, L.Martin, G.Machuca, E.Nevo, F.Lescop, E.Braun, D.A.Boschat, A.C.Sanquer, S.Guerrera, I.C.Revy, P.Parisot, M.Masson, C.Boddaert, N.Charbit, M.Decramer, S.Novo, R.Macher, M.A.Ranchin, B.Bacchetta, J.Laurent, A.Collardeau-Frachon, S.van Eerde, A.M.Hildebrandt, F.Magen, D.Antignac, C.van Tilbeurgh, H.Mollet, G.

(2019) Nat Commun 10: 3967-3967

  • DOI: 10.1038/s41467-019-11951-x
  • Primary Citation of Related Structures:  
    6GWJ

  • PubMed Abstract: 
  • N 6 -threonyl-carbamoylation of adenosine 37 of ANN-type tRNAs (t 6 A) is a universal modification essential for translational accuracy and efficiency. The t 6 A pathway uses two sequentially acting enzymes, YRDC and OSGEP, the latter being a subunit of the multiprotein KEOPS complex ...

    N 6 -threonyl-carbamoylation of adenosine 37 of ANN-type tRNAs (t 6 A) is a universal modification essential for translational accuracy and efficiency. The t 6 A pathway uses two sequentially acting enzymes, YRDC and OSGEP, the latter being a subunit of the multiprotein KEOPS complex. We recently identified mutations in genes encoding four out of the five KEOPS subunits in children with Galloway-Mowat syndrome (GAMOS), a clinically heterogeneous autosomal recessive disease characterized by early-onset steroid-resistant nephrotic syndrome and microcephaly. Here we show that mutations in YRDC cause an extremely severe form of GAMOS whereas mutations in GON7, encoding the fifth KEOPS subunit, lead to a milder form of the disease. The crystal structure of the GON7/LAGE3/OSGEP subcomplex shows that the intrinsically disordered GON7 protein becomes partially structured upon binding to LAGE3. The structure and cellular characterization of GON7 suggest its involvement in the cellular stability and quaternary arrangement of the KEOPS complex.


    Organizational Affiliation

    Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Université de Paris, Imagine Institute, Paris, France. geraldine.mollet@inserm.fr.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit LAGE3A [auth B]143Homo sapiensMutation(s): 0 
Gene Names: LAGE3DXS9879EESO3ITBA2
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Find proteins for Q14657 (Homo sapiens)
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Go to UniProtKB:  Q14657
PHAROS:  Q14657
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UniProt GroupQ14657
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit GON7B [auth D]106Homo sapiensMutation(s): 0 
Gene Names: GON7C14orf142
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Find proteins for Q9BXV9 (Homo sapiens)
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PHAROS:  Q9BXV9
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable tRNA N6-adenosine threonylcarbamoyltransferaseC [auth K]335Homo sapiensMutation(s): 0 
Gene Names: OSGEPGCPL1
EC: 2.3.1.234
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Find proteins for Q9NPF4 (Homo sapiens)
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Go to UniProtKB:  Q9NPF4
PHAROS:  Q9NPF4
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UniProt GroupQ9NPF4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.12α = 90
b = 105.12β = 90
c = 51.35γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2021-01-20
    Changes: Database references, Derived calculations, Structure summary