8Y2O | pdb_00008y2o

The Cryo-EM structure of human tRNA methyltransferase FTSJ1-THADA with substrate tRNA and S-adenosyl homocysteine (SAH)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico
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Literature

Structural insights into tRNA recognition of the human FTSJ1-THADA complex.

Ishiguro, K.Fujimura, A.Shirouzu, M.

(2025) Commun Biol 8: 893-893

  • DOI: https://doi.org/10.1038/s42003-025-08278-3
  • Primary Citation of Related Structures:  
    8Y2O

  • PubMed Abstract: 

    tRNA undergoes various post-transcriptional modifications in the anticodon loop. FTSJ1, a protein conserved among most eukaryotes, mediates 2'-O-methylations at position 32 (Nm32) or position 34 (Nm34), complexed with THADA or WDR6, respectively. These methylations are crucial for accurate translation and cellular growth. FTSJ1 mutations are associated with non-syndromic X-linked intellectual disability. Although the structure of the FTSJ1-WDR6 complex in yeast has been solved, the structural details of the FTSJ1-THADA complex formation and substrate recognition remain unclear. Herein, using cryo-electron microscopy, we solve the high-resolution structure of FTSJ1-THADA with or without a tRNA substrate. FTSJ1 binds to THADA via its C-terminal region, with a unique interaction mode distinct from the FTSJ1-WDR6 complex. The tRNA substrate is anchored inside THADA, and key THADA residues for THADA-tRNA interaction are identified via structural and biochemical analyses. These findings demonstrate how FTSJ1 and THADA form a complex to mediate Nm32 modification in various tRNAs.


  • Organizational Affiliation
    • Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (32-2'-O)-methyltransferase regulator THADA1,981Homo sapiensMutation(s): 0 
Gene Names: THADAGITAKIAA1767
UniProt & NIH Common Fund Data Resources
Find proteins for Q6YHU6 (Homo sapiens)
Explore Q6YHU6 
Go to UniProtKB:  Q6YHU6
PHAROS:  Q6YHU6
GTEx:  ENSG00000115970 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6YHU6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase347Homo sapiensMutation(s): 0 
Gene Names: FTSJ1JM23
EC: 2.1.1.205
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UET6 (Homo sapiens)
Explore Q9UET6 
Go to UniProtKB:  Q9UET6
PHAROS:  Q9UET6
GTEx:  ENSG00000068438 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UET6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
human cytoplasmic tRNA(Phe)76Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
E [auth B]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth C]
G [auth C]
H [auth C]
I [auth C]
J [auth C]
F [auth C],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
K [auth C],
L [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
MODEL REFINEMENTCoot0.9.5
RECONSTRUCTIONRELION3.1.3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP20cm0106179

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release