9X4G | pdb_00009x4g

Structure Of the KEOPS dimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Catalytic and regulatory basis of tRNA t 6 A modification by the KEOPS complex.

Zhou, L.Zhang, Z.Jin, M.Xie, D.Wen, H.Westhof, E.Lei, D.Zhang, W.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-73296-6
  • Primary Citation Related Structures: 
    9X4G, 9X4H

  • PubMed Abstract: 

    N 6 -threonylcarbamoyladenosine (t 6 A) at tRNA position 37 is essential for translational fidelity and cellular homeostasis. The multi-subunit KEOPS complex catalyzes t 6 A 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 t 6 A 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 t 6 A 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.


  • Organizational Affiliation
    • School of Life Sciences, State Key Laboratory of Natural Product Chemistry, Lanzhou University, Lanzhou, China.

Macromolecule Content 

  • Total Structure Weight: 195.77 kDa 
  • Atom Count: 11,768 
  • Modeled Residue Count: 1,518 
  • Deposited Residue Count: 1,776 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N(6)-L-threonylcarbamoyladenine synthase
A, E
337Caenorhabditis elegansMutation(s): 0 
Gene Names: CELE_Y71H2AM.1Y71H2AM.1
EC: 2.3.1.234
UniProt
Find proteins for Q9BL28 (Caenorhabditis elegans)
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UniProt GroupQ9BL28
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
non-specific serine/threonine protein kinase
B, F
245Caenorhabditis elegansMutation(s): 0 
Gene Names: CELE_F52C12.6F52C12.6
EC: 2.7.11.1
UniProt
Find proteins for B5WWL2 (Caenorhabditis elegans)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
EKC/KEOPS complex subunit TPRKB
C, G
183Caenorhabditis elegansMutation(s): 0 
Gene Names: CELE_W03F8.4W03F8.4
UniProt
Find proteins for O44566 (Caenorhabditis elegans)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
L antigen family member 3
D, H
123Caenorhabditis elegansMutation(s): 0 
Gene Names: CELE_F59A2.5F59A2.5
UniProt
Find proteins for Q21019 (Caenorhabditis elegans)
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina23JRRA1018

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release