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- EMDB-50536: Cryo-EM structure of the human KEOPS complex -

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Basic information

Entry
Database: EMDB / ID: EMD-50536
TitleCryo-EM structure of the human KEOPS complex
Map data
Sample
  • Complex: human KEOPS complex
    • Protein or peptide: EKC/KEOPS complex subunit TPRKB
    • Protein or peptide: EKC/KEOPS complex subunit TP53RK
    • Protein or peptide: Probable tRNA N6-adenosine threonylcarbamoyltransferase
    • Protein or peptide: EKC/KEOPS complex subunit LAGE3
    • Protein or peptide: EKC/KEOPS complex subunit GON7
KeywordsComplex t6A modification tRNA KEOPS Galloway-Mowat / RNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsCirio C / Fernandes CAH / Venien-Bryan C / Collinet B / Van Tilbeurgh H
Funding support France, 1 items
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 CAH / Dammak R / Venien-Bryan C / Mollet G / Zelie E / Malhao M / Arteni AA / Touboul D / Antignac C / Missoury S / Van Tilbeurgh H / Collinet B
History
DepositionJun 4, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50536.png

Downloads & links

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Map

FileDownload / File: emd_50536.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 320 pix.
= 246.4 Å		0.77 Å/pix.
x 320 pix.
= 246.4 Å		0.77 Å/pix.
x 320 pix.
= 246.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0311
Minimum - Maximum-0.09016638 - 0.23324765
Average (Standard dev.)0.00009253553 (±0.0058481363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 246.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: B-factor sharpened map

Fileemd_50536_additional_1.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map

Fileemd_50536_half_map_1.map
AnnotationSecond half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First half map

Fileemd_50536_half_map_2.map
AnnotationFirst half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human KEOPS complex

EntireName: human KEOPS complex
Components
  • Complex: human KEOPS complex
    • Protein or peptide: EKC/KEOPS complex subunit TPRKB
    • Protein or peptide: EKC/KEOPS complex subunit TP53RK
    • Protein or peptide: Probable tRNA N6-adenosine threonylcarbamoyltransferase
    • Protein or peptide: EKC/KEOPS complex subunit LAGE3
    • Protein or peptide: EKC/KEOPS complex subunit GON7

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Supramolecule #1: human KEOPS complex

SupramoleculeName: human KEOPS complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: EKC/KEOPS complex subunit TPRKB

MacromoleculeName: EKC/KEOPS complex subunit TPRKB / type: protein_or_peptide / ID: 1 / Details: N-ter His-tag followed by a TEV cleavage site / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.364695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHENL YFQGQLTHQL DLFPECRVTL LLFKDVKNAG DLRRKAMEGT IDGSLINPTV IVDPFQILVA ANKAVHLYKL GKMKTRTLS TEIIFNLSPN NNISEALKKF GISANDTSIL IVYIEEGEKQ INQEYLISQV EGHQVSLKNL PEIMNITEVK K IYKLSSQE ESIGTLLDAI ICRMSTKDVL

UniProtKB: EKC/KEOPS complex subunit TPRKB

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Macromolecule #2: EKC/KEOPS complex subunit TP53RK

MacromoleculeName: EKC/KEOPS complex subunit TP53RK / type: protein_or_peptide / ID: 2 / Details: N-ter His-tag followed by a TEV cleavage site / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.885266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQGAAARAT TPADGEEPAP EAEALAAARE RSSRFLSGLE LVKQGAEARV FRGRFQGRAA VIKHRFPKGY RHPALEARL GRRRTVQEAR ALLRCRRAGI SAPVVFFVDY ASNCLYMEEI EGSVTVRDYI QSTMETEKTP QGLSNLAKTI G QVLARMHD ...String:
MHHHHHHENL YFQGAAARAT TPADGEEPAP EAEALAAARE RSSRFLSGLE LVKQGAEARV FRGRFQGRAA VIKHRFPKGY RHPALEARL GRRRTVQEAR ALLRCRRAGI SAPVVFFVDY ASNCLYMEEI EGSVTVRDYI QSTMETEKTP QGLSNLAKTI G QVLARMHD EDLIHGDLTT SNMLLKPPLE QLNIVLIDFG LSFISALPED KGVDLYVLEK AFLSTHPNTE TVFEAFLKSY ST SSKKARP VLKKLDEVRL RGRKRSMVG

UniProtKB: EKC/KEOPS complex subunit TP53RK

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Macromolecule #3: Probable tRNA N6-adenosine threonylcarbamoyltransferase

MacromoleculeName: Probable tRNA N6-adenosine threonylcarbamoyltransferase
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: N6-L-threonylcarbamoyladenine synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.466805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPAVLGFEGS ANKIGVGVVR DGKVLANPRR TYVTPPGTGF LPGDTARHHR AVILDLLQEA LTESGLTSQD IDCIAYTKGP GMGAPLVSV AVVARTVAQL WNKPLVGVNH CIGHIEMGRL ITGATSPTVL YVSGGNTQVI AYSEHRYRIF GETIDIAVGN C LDRFARVL ...String:
MPAVLGFEGS ANKIGVGVVR DGKVLANPRR TYVTPPGTGF LPGDTARHHR AVILDLLQEA LTESGLTSQD IDCIAYTKGP GMGAPLVSV AVVARTVAQL WNKPLVGVNH CIGHIEMGRL ITGATSPTVL YVSGGNTQVI AYSEHRYRIF GETIDIAVGN C LDRFARVL KISNDPSPGY NIEQMAKRGK KLVELPYTVK GMDVSFSGIL SFIEDVAHRM LATGECTPED LCFSLQETVF AM LVEITER AMAHCGSQEA LIVGGVGCNV RLQEMMATMC QERGARLFAT DERFCIDNGA MIAQAGWEMF RAGHRTPLSD SGV TQRYRT DEVEVTWRD

UniProtKB: tRNA N6-adenosine threonylcarbamoyltransferase

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Macromolecule #4: EKC/KEOPS complex subunit LAGE3

MacromoleculeName: EKC/KEOPS complex subunit LAGE3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.82576 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRDADADAGG GADGGDGRGG HSCRGGVDTA AAPAGGAPPA HAPGPGRDAA SAARGSRMRP HIFTLSVPFP TPLEAEIAHG SLAPDAEPH QRVVGKDLTV SGRILVVRWK AEDCRLLRIS VINFLDQLSL VVRTMQRFGP PVSR

UniProtKB: EKC/KEOPS complex subunit LAGE3

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Macromolecule #5: EKC/KEOPS complex subunit GON7

MacromoleculeName: EKC/KEOPS complex subunit GON7 / type: protein_or_peptide / ID: 5 / Details: C-ter His-tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.697628 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MELLGEYVGQ EGKPQKLRVS CEAPGDGDPF QGLLSGVAQM KDMVTELFDP LVQGEVQHRV AAAPDEDLDG DDEDDAEDEN NIDNRTNFD GPSAKRPKTP SHHHHHH

UniProtKB: EKC/KEOPS complex subunit GON7

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.35 mg/mL
BufferpH: 7.5 / Component - Concentration: 20.0 mM / Component - Name: HEPES
Details: 20 mM HEPES pH 7.5, 50 mM NaCl, 5 mM 2-mercaptoethanol
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Details: twice 25 s
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting force 2, blotting time 8 s.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 14328 / Average exposure time: 2.16 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4)CTF estimation
cryoSPARC (ver. 4.2.1)CTF correction

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 214527
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6wqx

source_name: PDB, initial_model_type: experimental model

6gwj

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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