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- PDB-8y2o: The Cryo-EM structure of human tRNA methyltransferase FTSJ1-THADA... -

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Basic information

Entry
Database: PDB / ID: 8y2o
TitleThe Cryo-EM structure of human tRNA methyltransferase FTSJ1-THADA with substrate tRNA and S-adenosyl homocysteine (SAH)
Components
  • human cytoplasmic tRNA(Phe)
  • tRNA (32-2'-O)-methyltransferase regulator THADA
  • tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase
KeywordsRNA BINDING PROTEIN/RNA / tRNA modification enzymes / methyl transferases / tRNA-protein complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


tRNA 2'-O-methyltransferase activity / tRNA (guanosine(34)-2'-O)-methyltransferase activity / wobble position ribose methylation / tRNA (guanine) methyltransferase activity / tRNA (cytidine32/guanosine34-2'-O)-methyltransferase / tRNA nucleoside ribose methylation / tRNA methyltransferase activity / adaptive thermogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / tRNA modification in the nucleus and cytosol ...tRNA 2'-O-methyltransferase activity / tRNA (guanosine(34)-2'-O)-methyltransferase activity / wobble position ribose methylation / tRNA (guanine) methyltransferase activity / tRNA (cytidine32/guanosine34-2'-O)-methyltransferase / tRNA nucleoside ribose methylation / tRNA methyltransferase activity / adaptive thermogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / tRNA modification in the nucleus and cytosol / tRNA modification / tRNA methylation / S-adenosyl-L-methionine binding / lipid homeostasis / cytoplasmic side of endoplasmic reticulum membrane / enzyme regulator activity / neurogenesis / cytoplasmic translation / nucleus / cytosol / cytoplasm
Similarity search - Function
THADA/TRM732, DUF2428 / : / THADA/TRM732, DUF2428 / tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase TRM7 / : / Ribosomal RNA large subunit methyltransferase E / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Armadillo-type fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / : / RNA / RNA (> 10) / tRNA (32-2'-O)-methyltransferase regulator THADA / tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsIshiguro, K. / Fujimura, A. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20cm0106179 Japan
CitationJournal: Commun Biol / Year: 2025
Title: Structural insights into tRNA recognition of the human FTSJ1-THADA complex.
Authors: Kensuke Ishiguro / Atsushi Fujimura / Mikako Shirouzu /
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 ...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.
History
DepositionJan 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (32-2'-O)-methyltransferase regulator THADA
B: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase
C: human cytoplasmic tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,50212
Polymers285,8823
Non-polymers6209
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 , 2 types, 2 molecules AB

#1: Protein tRNA (32-2'-O)-methyltransferase regulator THADA / Gene inducing thyroid adenomas protein / Thyroid adenoma-associated protein


Mass: 223138.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THADA, GITA, KIAA1767 / Cell line (production host): FreeStyle HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q6YHU6
#2: Protein tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase / 2'-O-ribose RNA methyltransferase TRM7 homolog / Protein ftsJ homolog 1


Mass: 38224.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTSJ1, JM23 / Cell line (production host): FreeStyle HEK293F / Production host: Homo sapiens (human)
References: UniProt: Q9UET6, tRNA (cytidine32/guanosine34-2'-O)-methyltransferase

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RNA chain , 1 types, 1 molecules C

#3: RNA chain human cytoplasmic tRNA(Phe)


Mass: 24518.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 29540470

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Non-polymers , 3 types, 9 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg

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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: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA with substrate tRNA and S-adenosyl homocysteine (SAH)
Type: COMPLEX
Details: FTSJ1-THADA was expressed and purified from HEK293F cells. tRNA substrate was transcribed and purified in vitro. FTSJ1-THADA, tRNA and SAH were incubated before grid preparation.
Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: FreeStyle HEK293F
Buffer solutionpH: 7.5 / Details: The Buffer pH was adjusted to 7.6 using HCl.
Buffer component
IDConc.NameFormulaBuffer-ID
160 mMtris(hydroxymethyl)aminomethaneC4H11NO31
250 mMpotassium chlorideKCl1
375 mMsodium chlorideNaCl1
45 mMmagnesium chlorideMgCl21
51 mMdithiothreitolC4H10O2S21
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 1.2mg/ml FTSJ1-THADA was incubated with 2 fold molar tRNA and 1mM SAH.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 22969

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Processing

EM software
IDNameVersionCategory
1crYOLO1.8.2particle selection
4RELION3.1.3CTF correction
7UCSF Chimera1.14model fitting
8Coot0.9.5model fitting
10PHENIX1.18model refinement
11Coot0.9.5model refinement
12RELION3.1.3initial Euler assignment
13RELION3.1.3final Euler assignment
14RELION3.1.3classification
15RELION3.1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7275741
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1854516 / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Details: alphafold prediction was used as initial model of FTSJ1-THADA
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.66 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00817886
ELECTRON MICROSCOPYf_angle_d0.679424618
ELECTRON MICROSCOPYf_chiral_restr0.04462930
ELECTRON MICROSCOPYf_plane_restr0.00472831
ELECTRON MICROSCOPYf_dihedral_angle_d11.24282988

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