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- PDB-9x4h: Structure Of the KEOPS-tRNA -

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Basic information

Entry
Database: PDB / ID: 9x4h
TitleStructure Of the KEOPS-tRNA
Components
  • EKC/KEOPS complex subunit TPRKB
  • L antigen family member 3
  • N(6)-L-threonylcarbamoyladenine synthase
  • RNA (76-MER)
  • non-specific serine/threonine protein kinase
KeywordsTRANSFERASE/RNA / tRNA modification / t6A / KEOPS-tRNA complex / cryo-EM structure / substrate recognition / catalytic mechanism / regulation principle / 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
: / RNA / RNA (> 10) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsZhang, Z.L. / Zhou, L. / Jin, M.Q. / Lei, D.S. / Zhang, W.H.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data 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: N(6)-L-threonylcarbamoyladenine synthase
B: non-specific serine/threonine protein kinase
C: EKC/KEOPS complex subunit TPRKB
D: L antigen family member 3
E: L antigen family member 3
F: N(6)-L-threonylcarbamoyladenine synthase
T: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,5619
Polymers172,4837
Non-polymers782
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 6 molecules AFBCDE

#1: Protein N(6)-L-threonylcarbamoyladenine synthase / KAE1 / N6-L-threonylcarbamoyladenine synthase


Mass: 36859.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_Y71H2AM.1, Y71H2AM.1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BL28, N6-L-threonylcarbamoyladenine synthase
#2: Protein non-specific serine/threonine protein kinase / BUD32


Mass: 27544.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_F52C12.6, F52C12.6 / Production host: Escherichia coli (E. coli)
References: UniProt: B5WWL2, non-specific serine/threonine protein kinase
#3: Protein EKC/KEOPS complex subunit TPRKB / CGI121


Mass: 20215.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_W03F8.4, W03F8.4 / Production host: Escherichia coli (E. coli) / References: UniProt: O44566
#4: Protein L antigen family member 3 / PCC1


Mass: 13223.827 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_F59A2.5, F59A2.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21019

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RNA chain / Non-polymers , 2 types, 3 molecules T

#5: RNA chain RNA (76-MER)


Mass: 24555.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli)
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: CeKEOPS-tRNA / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123388 / Symmetry type: POINT
RefinementHighest resolution: 3.36 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410436
ELECTRON MICROSCOPYf_angle_d0.69514436
ELECTRON MICROSCOPYf_dihedral_angle_d15.5974163
ELECTRON MICROSCOPYf_chiral_restr0.0451734
ELECTRON MICROSCOPYf_plane_restr0.0051557

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