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- EMDB-61703: The Cryo-EM structure of human tRNA methyltransferase FTSJ1-THADA... -

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Basic information

Entry
Database: EMDB / ID: EMD-61703
TitleThe Cryo-EM structure of human tRNA methyltransferase FTSJ1-THADA (Class 2b)
Map data
Sample
  • Complex: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA
    • Protein or peptide: THADA
    • Protein or peptide: FTSJ1
KeywordstRNA modification enzymes / methyl transferases / RNA BINDING PROTEIN
Function / homologytRNA (cytidine32/guanosine34-2'-O)-methyltransferase / Isoform 1 of tRNA (32-2'-O)-methyltransferase regulator THADA / Isoform 1 of tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.06 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
DepositionSep 26, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61703.png

Downloads & links

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Map

FileDownload / File: emd_61703.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 260 pix.
= 215.41 Å		0.83 Å/pix.
x 260 pix.
= 215.41 Å		0.83 Å/pix.
x 260 pix.
= 215.41 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00965
Minimum - Maximum-0.01652493 - 0.03894431
Average (Standard dev.)-0.00004880328 (±0.0020104412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 215.40999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61703_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61703_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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

EntireName: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA
Components
  • Complex: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA
    • Protein or peptide: THADA
    • Protein or peptide: FTSJ1

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

SupramoleculeName: The Cryo-EM structure of tRNA methyltransferase FTSJ1-THADA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: FTSJ1-THADA was expressed and purified from HEK293F cells.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: THADA

MacromoleculeName: THADA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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: Isoform 1 of tRNA (32-2'-O)-methyltransferase regulator THADA

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Macromolecule #2: FTSJ1

MacromoleculeName: FTSJ1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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: Isoform 1 of tRNA (cytidine(32)/guanosine(34)-2'-O)-methyltransferase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.4 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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 14544 / 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 / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5314179
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 83420
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: 61868 / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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