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- EMDB-66545: Structure Of the KEOPS-tRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-66545
TitleStructure Of the KEOPS-tRNA
Map data
Sample
  • Complex: CeKEOPS-tRNA
    • Protein or peptide: N(6)-L-threonylcarbamoyladenine synthase
    • Protein or peptide: non-specific serine/threonine protein kinase
    • Protein or peptide: EKC/KEOPS complex subunit TPRKB
    • Protein or peptide: L antigen family member 3
    • RNA: RNA (76-MER)
  • Ligand: POTASSIUM ION
KeywordstRNA modification / t6A / KEOPS-tRNA complex / cryo-EM structure / substrate recognition / catalytic mechanism / regulation principle / TRANSFERASE/RNA / TRANSFERASE-RNA complex
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 / tRNA processing / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / metal ion binding ...N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine metabolic process / tRNA threonylcarbamoyladenosine modification / tRNA processing / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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 / : / RIO domain / ATPase, nucleotide binding domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
non-specific serine/threonine protein kinase / EKC/KEOPS complex subunit TPRKB / L antigen family member 3 / N(6)-L-threonylcarbamoyladenine synthase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsZhang ZL / Zhou L / Jin MQ / Lei DS / Zhang WH
Funding support China, 1 items
OrganizationGrant numberCountry
Other government23JRRA1018 China
CitationJournal: Nat Commun / Year: 2026
Title: Catalytic and regulatory basis of tRNA tA modification by the KEOPS complex.
Authors: Li Zhou / Zelin Zhang / Mengqi Jin / Dengmiao Xie / Han Wen / Eric Westhof / Dongsheng Lei / Wenhua Zhang /
Abstract: N-threonylcarbamoyladenosine (tA) at tRNA position 37 is essential for translational fidelity and cellular homeostasis. The multi-subunit KEOPS complex catalyzes tA formation in Archaea and Eukarya. ...N-threonylcarbamoyladenosine (tA) at tRNA position 37 is essential for translational fidelity and cellular homeostasis. The multi-subunit KEOPS complex catalyzes tA formation in Archaea and Eukarya. Here we present cryo-EM structures of C. elegans KEOPS in its apo and tRNA-bound states. tRNA binding induces concerted conformational rearrangements, distorting the anticodon loop to project A37 into the Kae1 active site. Kae1 recognizes the conserved G10-C25 pair and 36-UAA-38 motif. Bud32 directly contacts the anticodon and acceptor arms, coupling ATP hydrolysis to tA catalysis in the distant Kae1 active site through long-range conformational changes. Cgi121 enhances catalytic efficiency through cooperative binding with Bud32 and the tRNA 3' CCA. Pcc1 stabilizes the anticodon loop and mediates KEOPS dimerization, enhancing tRNA binding and tA activity. GAMOS-associated mutations cluster at functional hotspots within the KEOPS-tRNA complex. This study provides a structural framework for understanding KEOPS mechanism and its cellular roles.
History
DepositionOct 10, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66545.png

Downloads & links

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Map

FileDownload / File: emd_66545.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.104 Å		0.83 Å/pix.
x 384 pix.
= 319.104 Å		0.83 Å/pix.
x 384 pix.
= 319.104 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-0.15275417 - 14.525971
Average (Standard dev.)-0.06265605 (±0.28105232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66545_msk_1.map
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Half map: #2

Fileemd_66545_half_map_1.map
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Half map: #1

Fileemd_66545_half_map_2.map
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Sample components

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Entire : CeKEOPS-tRNA

EntireName: CeKEOPS-tRNA
Components
  • Complex: CeKEOPS-tRNA
    • Protein or peptide: N(6)-L-threonylcarbamoyladenine synthase
    • Protein or peptide: non-specific serine/threonine protein kinase
    • Protein or peptide: EKC/KEOPS complex subunit TPRKB
    • Protein or peptide: L antigen family member 3
    • RNA: RNA (76-MER)
  • Ligand: POTASSIUM ION

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Supramolecule #1: CeKEOPS-tRNA

SupramoleculeName: CeKEOPS-tRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: N(6)-L-threonylcarbamoyladenine synthase

MacromoleculeName: N(6)-L-threonylcarbamoyladenine synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: N6-L-threonylcarbamoyladenine synthase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 36.859742 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVCVIGIEGS ANKIGVGIIR DGVVLSNPRA TFHAPPGEGF RPTETAQHHR QQIVRLVGEA IKLANIQNPE LEIDGIAYTK GPGMGAPLQ VGAIVARTLS LTWKKPIIPV NHCVGHIEMG RLITGADNPV VLYVSGGNTQ VISYTKKRYR IFGETIDIAV G NCLDRFAR ...String:
MVCVIGIEGS ANKIGVGIIR DGVVLSNPRA TFHAPPGEGF RPTETAQHHR QQIVRLVGEA IKLANIQNPE LEIDGIAYTK GPGMGAPLQ VGAIVARTLS LTWKKPIIPV NHCVGHIEMG RLITGADNPV VLYVSGGNTQ VISYTKKRYR IFGETIDIAV G NCLDRFAR VLKLPNAPSP GYNIEQLAKN GKKLMELPYS VKGMDVSLSG ILSLIEKKAP KLIESGDFTP EDLCFSLQET VF AMLIEIT ERAMAHTSSK ELLIVGGVGC NLRLQEMASA MCAERGAHLF ATDERFCIDN GAMIARAGEL MLASGMRFDL RKT TTTQRY RTDQVHVEWR D

UniProtKB: N(6)-L-threonylcarbamoyladenine synthase

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Macromolecule #2: non-specific serine/threonine protein kinase

MacromoleculeName: non-specific serine/threonine protein kinase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 27.544473 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTAATTSSDS EGEMDFETTI ETGFGYQIDG LLYQGAEAKV TKCIWLGRQA IIKERFSKGY RHPTLDTQLN KARTKQEIRG LNKARELGI HVPAVYFIDN EKNQLIMEFV PGSTAKNWIS QLNPADFDAK TREFGQIFGE KLGKLHRGGL IHGDLTTSNI I LRDDDLQK ...String:
MTAATTSSDS EGEMDFETTI ETGFGYQIDG LLYQGAEAKV TKCIWLGRQA IIKERFSKGY RHPTLDTQLN KARTKQEIRG LNKARELGI HVPAVYFIDN EKNQLIMEFV PGSTAKNWIS QLNPADFDAK TREFGQIFGE KLGKLHRGGL IHGDLTTSNI I LRDDDLQK MTFIDFGLSS QGKVTPEEKG VDLYVLERAV ISTHDKCAAL IEGLMEGYKK ADGKQFVAVE KKLNEIRLRG RK RDMIG

UniProtKB: non-specific serine/threonine protein kinase

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Macromolecule #3: EKC/KEOPS complex subunit TPRKB

MacromoleculeName: EKC/KEOPS complex subunit TPRKB / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 20.215439 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKHSHLYELQ PDPYDFTQRK TCRVCLFKDV KNAAELSQQL KEGKIDAALI RAELVLEPFV LLAAANRAVH QSAHNRMSCR SLAAELVYS LSPSRNITDS LVTFGIAEHS TAIIAAIFDD DSGKAMKKLA KAIKGTPVPL MEGLPKFANV NMIKKVYQVG N PAFVEEGL SDHIVSRMVS KDFVS

UniProtKB: EKC/KEOPS complex subunit TPRKB

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Macromolecule #4: L antigen family member 3

MacromoleculeName: L antigen family member 3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 13.223827 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEVDTSSSSS SEDECDPSSP STAYIHSASV RLSVGTEEAA RTVADVIKID KEPRRSGARR EVCSEGEFVV IKIESKDPKS LSKSIANAV DMIDLSVKTI KLCENLGKSK ENGLKRKLSN GSQA

UniProtKB: L antigen family member 3

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Macromolecule #5: RNA (76-MER)

MacromoleculeName: RNA (76-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 24.555592 KDa
SequenceString:
GCUUCCGUGG CGCAAUAGGC AGCGCGUUCG GCUGUUAACC GAAAGGUUGG UGGUUCGAGC CCACCCGGGA GCGCCA

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Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model#0 - Type of model: NONE / #1 - Type of model: NONE / #2 - Type of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123388
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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