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- SASDFL8: GON7, the fifth subunit of human KEOPS, bound to LAGE3-OSGEP (EKC... -

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Basic information

Entry
Database: SASBDB / ID: SASDFL8
SampleGON7, the fifth subunit of human KEOPS, bound to LAGE3-OSGEP (EKC/KEOPS complex subunit:Probable tRNA N6-adenosine threonylcarbamoyltransferase)
  • EKC/KEOPS complex subunit GON7 (protein), GON7, Homo sapiens
  • EKC/KEOPS complex subunit LAGE3 (protein), LAGE3, Homo sapiens
  • Probable tRNA N6-adenosine threonylcarbamoyltransferase (protein), OSGEP, Homo sapiens
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / tRNA modification in the nucleus and cytosol / nuclear speck / nucleolus / nucleoplasm / nucleus / metal ion binding ...N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / tRNA modification in the nucleus and cytosol / nuclear speck / nucleolus / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
EKC/KEOPS complex subunit GON7, metazoa / Domain of unknown function (DUF4611) / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
: / EKC/KEOPS complex subunit GON7 / tRNA N6-adenosine threonylcarbamoyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
CitationDate: 2019 Dec
Title: Defects in t6A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome
Authors: 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 / Boschat A ...Authors: 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 / Boschat A / Sanquer S / Guerrera I / Revy P / Parisot M / Masson C / Boddaert N / Charbit M / Decramer S / Novo R / Macher M / Ranchin B / Bacchetta J / Laurent A / Collardeau-Frachon S / van Eerde A / Hildebrandt F / Magen D / Antignac C / van Tilbeurgh H
Contact author
  • sophia missoury (I2BC-CNRS, Paris, France)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #3207
Type: atomic / Chi-square value: 0.308 / P-value: 0.001285
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: GON7, the fifth subunit of human KEOPS, bound to LAGE3-OSGEP (EKC/KEOPS complex subunit:Probable tRNA N6-adenosine threonylcarbamoyltransferase)
Specimen concentration: 1.48 mg/ml / Entity id: 1759 / 1760 / 1761
BufferName: 20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol / pH: 6.5
Entity #1759Name: GON7 / Type: protein / Description: EKC/KEOPS complex subunit GON7 / Formula weight: 11.682 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q9BXV9
Sequence:
MELLGEYVGQ EGKPQKLRVS CEAPGDGDPF QGLLSGVAQM KDMVTELFDP LVQGEVQHRV AAAPDEDLDG DDEDDAEDEN NIDNRTNFDG PSAKRPKTPS HHHHHH
Entity #1760Name: LAGE3 / Type: protein / Description: EKC/KEOPS complex subunit LAGE3 / Formula weight: 14.804 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: 1-143
Sequence:
MRDADADAGG GADGGDGRGG HSCRGGVDTA AAPAGGAPPA HAPGPGRDAA SAARGSRMRP HIFTLSVPFP TPLEAEIAHG SLAPDAEPHQ RVVGKDLTVS GRILVVRWKA EDCRLLRISV INFLDQLSLV VRTMQRFGPP VSR
Entity #1761Name: OSGEP / Type: protein
Description: Probable tRNA N6-adenosine threonylcarbamoyltransferase
Formula weight: 36.426 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q9NPF4
Sequence: MPAVLGFEGS ANKIGVGVVR DGKVLANPRR TYVTPPGTGF LPGDTARHHR AVILDLLQEA LTESGLTSQD IDCIAYTKGP GMGAPLVSVA VVARTVAQLW NKPLVGVNHC IGHIEMGRLI TGATSPTVLY VSGGNTQVIA YSEHRYRIFG ETIDIAVGNC LDRFARVLKI ...Sequence:
MPAVLGFEGS ANKIGVGVVR DGKVLANPRR TYVTPPGTGF LPGDTARHHR AVILDLLQEA LTESGLTSQD IDCIAYTKGP GMGAPLVSVA VVARTVAQLW NKPLVGVNHC IGHIEMGRLI TGATSPTVLY VSGGNTQVIA YSEHRYRIFG ETIDIAVGNC LDRFARVLKI SNDPSPGYNI EQMAKRGKKL VELPYTVKGM DVSFSGILSF IEDVAHRMLA TGECTPEDLC FSLQETVFAM LVEITERAMA HCGSQEALIV GGVGCNVRLQ EMMATMCQER GARLFATDER FCIDNGAMIA QAGWEMFRAG HRTPLSDSGV TQRYRTDEVE VTWRD

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Experimental information

BeamInstrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 1.8 mm
DetectorName: AVIEX PCCD170170 / Type: CCD
Scan
Title: GON7, the fifth subunit of human KEOPS, bound to LAGE3-OSGEP (EKC/KEOPS complex subunit:Probable tRNA N6-adenosine threonylcarbamoyltransferase)
Measurement date: May 12, 2017 / Cell temperature: 15 °C / Exposure time: 1 sec. / Number of frames: 255 / Unit: 1/A /
MinMax
Q0.0101 0.5003
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 685 /
MinMax
Q0.0101436 0.400022
P(R) point1 685
R0 115
Result
Type of curve: sec
Comments: The scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. SAXS data were normalized to the intensity of the incident beam, averaged and background ...Comments: The scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. SAXS data were normalized to the intensity of the incident beam, averaged and background subtracted using the program US-SOMO. Frames were examined individually and 21 identical frames were averaged and further processed. The corresponding SEC-elution concentration was approximately 0.35 mg/mL. The complex is constituted of one monomer of OSGEP, one monomer of LAGE3 and one monomer of GON7. Molecular mass was obtained using the Bayesian inference approach proposed in PRIMUS/qt, which combines four concentration independent MM estimators: M=59.5 kDa within the credibility interval [57.5-64.5].
ExperimentalStandardPorod
MW59.5 kDa58.5 kDa57 kDa
Volume--91 nm3

P(R)GuinierGuinier error
Forward scattering, I00.01634 0.01625 2.0E-5
Radius of gyration, Rg3.14 nm3.06 nm0.06

MinMax
D-11.5
Guinier point1 58

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