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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit LAGE3A [auth B]143Homo sapiensMutation(s): 0 
Gene Names: LAGE3DXS9879EESO3ITBA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14657 (Homo sapiens)
Explore Q14657 
Go to UniProtKB:  Q14657
PHAROS:  Q14657
GTEx:  ENSG00000196976 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14657
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit GON7B [auth D]106Homo sapiensMutation(s): 0 
Gene Names: GON7C14orf142
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXV9 (Homo sapiens)
Explore Q9BXV9 
Go to UniProtKB:  Q9BXV9
PHAROS:  Q9BXV9
GTEx:  ENSG00000170270 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXV9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Probable tRNA N6-adenosine threonylcarbamoyltransferaseC [auth K]335Homo sapiensMutation(s): 0 
Gene Names: OSGEPGCPL1
EC: 2.3.1.234
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF4 (Homo sapiens)
Explore Q9NPF4 
Go to UniProtKB:  Q9NPF4
PHAROS:  Q9NPF4
GTEx:  ENSG00000092094 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPF4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
F [auth K]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K,
L [auth K],
M [auth K]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth B],
E [auth D],
H [auth K],
I [auth K],
J [auth K]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth K]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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

View Full Validation Report



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