[English] 日本語
Yorodumi
- EMDB-38859: The Cryo-EM structure of human tRNA methyltransferase FTSJ1-THADA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38859
TitleThe Cryo-EM structure of human tRNA methyltransferase FTSJ1-THADA with substrate tRNA and S-adenosyl homocysteine (SAH)
Map data
Sample
  • Complex: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA with substrate tRNA and S-adenosyl homocysteine (SAH)
    • Protein or peptide: tRNA (32-2'-O)-methyltransferase regulator THADA
    • Protein or peptide: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase
    • RNA: human cytoplasmic tRNA(Phe)
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: MAGNESIUM ION
KeywordstRNA 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
tRNA (32-2'-O)-methyltransferase regulator THADA / tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsIshiguro K / Fujimura A / Shirouzu M
Funding support Japan, 1 items
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, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38859.png

Downloads & links

-
Map

FileDownload / File: emd_38859.map.gz / Format: CCP4 / Size: 67 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 260 pix.
= 215.8 Å		0.83 Å/pix.
x 260 pix.
= 215.8 Å		0.83 Å/pix.
x 260 pix.
= 215.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0126
Minimum - Maximum-0.045098502 - 0.105760686
Average (Standard dev.)0.00019207333 (±0.0036428273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 215.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_38859_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38859_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA with ...

EntireName: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA with substrate tRNA and S-adenosyl homocysteine (SAH)
Components
  • Complex: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA with substrate tRNA and S-adenosyl homocysteine (SAH)
    • Protein or peptide: tRNA (32-2'-O)-methyltransferase regulator THADA
    • Protein or peptide: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase
    • RNA: human cytoplasmic tRNA(Phe)
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA with ...

SupramoleculeName: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA with substrate tRNA and S-adenosyl homocysteine (SAH)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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.
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: tRNA (32-2'-O)-methyltransferase regulator THADA

MacromoleculeName: tRNA (32-2'-O)-methyltransferase regulator THADA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 223.138812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKS AWSHPQFEKG AENLYFQGMG VKKKKEMQVA ALTICHQDLE TLKSFADVEG KNLASLLLHC VQLTDGVSQI HYIKQIVPL LEKADKNGMC DPTIQSCLDI LAGIYLSLSL KNPLKKVLAS SLNSLPDFFL PEAMHRFTSR LQEELNTTDL Y SYRKVTDN ...String:
MDYKDDDDKS AWSHPQFEKG AENLYFQGMG VKKKKEMQVA ALTICHQDLE TLKSFADVEG KNLASLLLHC VQLTDGVSQI HYIKQIVPL LEKADKNGMC DPTIQSCLDI LAGIYLSLSL KNPLKKVLAS SLNSLPDFFL PEAMHRFTSR LQEELNTTDL Y SYRKVTDN ISSCMENFNL GRASVNNLLK NVLHFLQKSL IEILEENRKC AGNHIIQTQL MNDLLVGIRV SMMLVQKVQD FQ GNLWKTS DSPIWQNMCG LLSIFTKVLS DDDLLQTVQS TSGLAIILFI KTMFHPSEKI PHLISSVLLR SVDCTSVPEW FMS SCRSLC CGDISQSAVL FLCQGTLAML DWQNGSMGRS GEALLLDTAH VLFTLSSQIK EPTLEMFLSR ILASWTNSAI QVLE SSSPS LTDSLNGNSS IVGRLLEYVY THWEHPLDAL RHQTKIMFKN LLQMHRLTVE GADFVPDPFF VELTESLLRL EWHIK GKYT CLGCLVECIG VEHILAIDKT IPSQILEVMG DQSLVPYASD LLETMFRNHK SHLKSQTAES SWIDQWHETW VSPLLF ILC EGNLDQKSYV IDYYLPKLLS YSPESLQYMV KILQTSIDAK TGQEQSFPSL GSCNSRGALG ALMACLRIAR AHGHLQS AT DTWENLVSDA RIKQGLIHQH CQVRIDTLGL LCESNRSTEI VSMEEMQWIQ FFITYNLNSQ SPGVRQQICS LLKKLFCR I QESSQVLYKL EQSKSKREPE NELTKQHPSV SLQQYKNFMS SICNSLFEAL FPGSSYSTRF SALTILGSIA EVFHVPEGR IYTVYQLSHD IDVGRFQTLM ECFTSTFEDV KILAFDLLMK LSKTAVHFQD SGKLQGLFQA ALELSTSTKP YDCVTASYLL NFLIWQDAL PSSLSAYLTQ QVACDNGDRP AAVVERNTLM VIKCLMENLE EEVSQAENSL LQAAAAFPMY GRVHCITGAL Q KLSLNSLQ LVSEWRPVVE KLLLMSYRLS TVVSPVIQSS SPEGLIPMDT DSESASRLQM ILNEIQPRDT NDYFNQAKIL KE HDSFDMK DLNASVVNID TSTEIKGKEV KTCDVTAQMV LVCCWRSMKE VALLLGMLCQ LLPMQPVPES SDGLLTVEQV KEI GDYFKQ HLLQSRHRGA FELAYTGFVK LTEVLNRCPN VSLQKLPEQW LWSVLEEIKC SDPSSKLCAT RRSAGIPFYI QALL ASEPK KGRMDLLKIT MKELISLAGP TDDIQSTVPQ VHALNILRAL FRDTRLGENI IPYVADGAKA AILGFTSPVW AVRNS STLL FSALITRIFG VKRAKDEHSK TNRMTGREFF SRFPELYPFL LKQLETVANT VDSDMGEPNR HPSMFLLLLV LERLYA SPM DGTSSALSMG PFVPFIMRCG HSPVYHSREM AARALVPFVM IDHIPNTIRT LLSTLPSCTD QCFRQNHIHG TLLQVFH LL QAYSDSKHGT NSDFQHELTD ITVCTKAKLW LAKRQNPCLV TRAVYIDILF LLTCCLNRSA KDNQPVLESL GFWEEVRG I ISGSELITGF PWAFKVPGLP QYLQSLTRLA IAAVWAAAAK SGERETNVPI SFSQLLESAF PEVRSLTLEA LLEKFLAAA SGLGEKGVPP LLCNMGEKFL LLAMKENHPE CFCKILKILH CMDPGEWLPQ TEHCVHLTPK EFLIWTMDIA SNERSEIQSV ALRLASKVI SHHMQTCVEN RELIAAELKQ WVQLVILSCE DHLPTESRLA VVEVLTSTTP LFLTNPHPIL ELQDTLALWK C VLTLLQSE EQAVRDAATE TVTTAMSQEN TCQSTEFAFC QVDASIALAL ALAVLCDLLQ QWDQLAPGLP ILLGWLLGES DD LVACVES MHQVEEDYLF EKAEVNFWAE TLIFVKYLCK HLFCLLSKSG WRPPSPEMLC HLQRMVSEQC HLLSQFFREL PPA AEFVKT VEFTRLRIQE ERTLACLRLL AFLEGKEGED TLVLSVWDSY AESRQLTLPR TEAAC

UniProtKB: tRNA (32-2'-O)-methyltransferase regulator THADA

-
Macromolecule #2: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase

MacromoleculeName: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: tRNA (cytidine32/guanosine34-2'-O)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.224223 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG AENLYFQGMG RTSKDKRDVY YRLAKENGWR ARSAFKLLQL DKEFQLFQGV TRAVDLCAAP GSWSQVLSQK IGGQGSGHV VAVDLQAMAP LPGVVQIQGD ITQLSTAKEI IQHFKGCPAD LVVCDGAPDV TGLHDVDEYM QAQLLLAALN I ATHVLKPG ...String:
MDYKDDDDKG AENLYFQGMG RTSKDKRDVY YRLAKENGWR ARSAFKLLQL DKEFQLFQGV TRAVDLCAAP GSWSQVLSQK IGGQGSGHV VAVDLQAMAP LPGVVQIQGD ITQLSTAKEI IQHFKGCPAD LVVCDGAPDV TGLHDVDEYM QAQLLLAALN I ATHVLKPG GCFVAKIFRG RDVTLLYSQL QVFFSSVLCA KPRSSRNSSI EAFAVCQGYD PPEGFIPDLS KPLLDHSYDP DF NQLDGPT RIIVPFVTCG DLSSYDSDRS YPLDLEGGSE YKYTPPTQPP ISPPYQEACT LKRKGQLAKE IRPQDCPISR VDT FPQPLA APQCHTLLAP EMEDNEMSCS P

UniProtKB: tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase

-
Macromolecule #3: human cytoplasmic tRNA(Phe)

MacromoleculeName: human cytoplasmic tRNA(Phe) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.51857 KDa
SequenceString:
GCCGAAAUAG CUCAGUUGGG AGAGCGUUAG ACUGAAGAUC UAAAGGUCCC UGGUUCGAUC CCGGGUUUCG GCACCA

GENBANK: GENBANK: AC093719.26

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #5: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
60.0 mMC4H11NO3tris(hydroxymethyl)aminomethane
50.0 mMKClpotassium chloride
75.0 mMNaClsodium chloride
5.0 mMMgCl2magnesium chloride
1.0 mMC4H10O2S2dithiothreitol

Details: The Buffer pH was adjusted to 7.6 using HCl.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details1.2mg/ml FTSJ1-THADA was incubated with 2 fold molar tRNA and 1mM SAH.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 22969 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 7275741
CTF correctionSoftware - Name: RELION (ver. 3.1.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: using de novo 3D initial map generated by relion
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 1854516
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 10 / Avg.num./class: 226983 / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Detailsalphafold prediction was used as initial model of FTSJ1-THADA
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8y2o:
The Cryo-EM structure of human tRNA methyltransferase FTSJ1-THADA with substrate tRNA and S-adenosyl homocysteine (SAH)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more