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- PDB-9fl9: Cryo-EM structure of the human KEOPS complex -

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Basic information

Entry
Database: PDB / ID: 9fl9
TitleCryo-EM structure of the human KEOPS complex
Components
  • EKC/KEOPS complex subunit GON7
  • EKC/KEOPS complex subunit LAGE3
  • EKC/KEOPS complex subunit TP53RK
  • EKC/KEOPS complex subunit TPRKB
  • Probable tRNA N6-adenosine threonylcarbamoyltransferase
KeywordsRNA BINDING PROTEIN / Complex t6A modification tRNA KEOPS Galloway-Mowat
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine metabolic process / tRNA threonylcarbamoyladenosine modification / Hydrolases; Acting on acid anhydrides / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA processing / regulation of signal transduction by p53 class mediator ...N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine metabolic process / tRNA threonylcarbamoyladenosine modification / Hydrolases; Acting on acid anhydrides / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA processing / regulation of signal transduction by p53 class mediator / p53 binding / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / nuclear body / hydrolase activity / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleolus / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
EKC/KEOPS complex subunit GON7, metazoa / Domain of unknown function (DUF4611) / Lipopolysaccharide kinase (Kdo/WaaP) family / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Peptidase M22, conserved site / Glycoprotease family signature. ...EKC/KEOPS complex subunit GON7, metazoa / Domain of unknown function (DUF4611) / Lipopolysaccharide kinase (Kdo/WaaP) family / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / CTAG/Pcc1 family / Transcription factor Pcc1 / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
EKC/KEOPS complex subunit LAGE3 / EKC/KEOPS complex subunit TP53RK / EKC/KEOPS complex subunit GON7 / tRNA N6-adenosine threonylcarbamoyltransferase / EKC/KEOPS complex subunit TPRKB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsCirio, C. / Fernandes, C.A.H. / Venien-Bryan, C. / Collinet, B. / Van Tilbeurgh, H.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Cryo-EM structure of the human KEOPS complex
Authors: Cirio, C. / Auxilien, S. / Liger, D. / Fernandes, C.A.H. / Dammak, R. / Venien-Bryan, C. / Mollet, G. / Zelie, E. / Malhao, M. / Arteni, A.A. / Touboul, D. / Antignac, C. / Missoury, S. / ...Authors: Cirio, C. / Auxilien, S. / Liger, D. / Fernandes, C.A.H. / Dammak, R. / Venien-Bryan, C. / Mollet, G. / Zelie, E. / Malhao, M. / Arteni, A.A. / Touboul, D. / Antignac, C. / Missoury, S. / Van Tilbeurgh, H. / Collinet, B.
History
DepositionJun 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EKC/KEOPS complex subunit TPRKB
B: EKC/KEOPS complex subunit TP53RK
C: Probable tRNA N6-adenosine threonylcarbamoyltransferase
D: EKC/KEOPS complex subunit LAGE3
E: EKC/KEOPS complex subunit GON7


Theoretical massNumber of molelcules
Total (without water)114,2405
Polymers114,2405
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-50 kcal/mol
Surface area38880 Å2

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Components

#1: Protein EKC/KEOPS complex subunit TPRKB / PRPK-binding protein / TP53RK-binding protein


Mass: 21364.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-ter His-tag followed by a TEV cleavage site / Source: (gene. exp.) Homo sapiens (human) / Gene: TPRKB, CGI-121, My019 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C4
#2: Protein EKC/KEOPS complex subunit TP53RK / Atypical serine/threonine protein kinase TP53RK / Nori-2 / TP53-regulating kinase / p53-related protein kinase


Mass: 29885.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-ter His-tag followed by a TEV cleavage site / Source: (gene. exp.) Homo sapiens (human) / Gene: TP53RK, C20orf64, PRPK / Production host: Escherichia coli (E. coli)
References: UniProt: Q96S44, Hydrolases; Acting on acid anhydrides, non-specific serine/threonine protein kinase
#3: Protein Probable tRNA N6-adenosine threonylcarbamoyltransferase / N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / O-sialoglycoprotein endopeptidase / ...N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / O-sialoglycoprotein endopeptidase / hOSGEP / t(6)A37 threonylcarbamoyladenosine biosynthesis protein OSGEP / tRNA threonylcarbamoyladenosine biosynthesis protein OSGEP


Mass: 36466.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSGEP, GCPL1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NPF4, N6-L-threonylcarbamoyladenine synthase
#4: Protein EKC/KEOPS complex subunit LAGE3 / L antigen family member 3 / Protein ESO-3 / Protein ITBA2


Mass: 14825.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAGE3, DXS9879E, ESO3, ITBA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14657
#5: Protein EKC/KEOPS complex subunit GON7


Mass: 11697.628 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-ter His-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: GON7, C14orf142 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXV9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human KEOPS complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Details: 20 mM HEPES pH 7.5, 50 mM NaCl, 5 mM 2-mercaptoethanol
Buffer componentConc.: 20 mM / Name: HEPES
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: twice 25 s / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blotting force 2, blotting time 8 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.16 sec. / Electron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14328
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.2.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correctionCTF estimation
5cryoSPARC4.2.1CTF correctionCTF correction
8PHENIX1.20.1_4487model fitting
9UCSF Chimeramodel fitting
10NAMD1model fittingOn-line version of NAMDinator
12cryoSPARC4.2.1initial Euler assignment
13cryoSPARC4.2.1final Euler assignment
15cryoSPARC4.2.13D reconstruction
16PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214527 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16WQX

6wqx

16WQX1PDBexperimental model
26GWJ

6gwj

16GWJ2PDBexperimental model

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