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- EMDB-58360: Human tRNA ligase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-58360
TitleHuman tRNA ligase complex
Map data
Sample
  • Complex: tRNA ligase complex
    • Protein or peptide: Ashwin
    • Protein or peptide: Protein FAM98B
    • Protein or peptide: RNA transcription, translation and transport factor protein
    • Protein or peptide: ATP-dependent RNA helicase DDX1,Green fluorescent protein
    • Protein or peptide: RNA-splicing ligase RtcB homolog
  • Ligand: MAGNESIUM ION
Keywordsligase / tRNA
Function / homology
Function and homology information


tRNA exon ligation / cleavage body / tRNA-splicing ligase complex / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / RNA splicing, via endonucleolytic cleavage and ligation / mRNA splicing, via endonucleolytic cleavage and ligation / DNA/RNA helicase activity / tRNA splicing, via endonucleolytic cleavage and ligation / protein localization to cytoplasmic stress granule ...tRNA exon ligation / cleavage body / tRNA-splicing ligase complex / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / RNA splicing, via endonucleolytic cleavage and ligation / mRNA splicing, via endonucleolytic cleavage and ligation / DNA/RNA helicase activity / tRNA splicing, via endonucleolytic cleavage and ligation / protein localization to cytoplasmic stress granule / RNA transport / nuclease activity / positive regulation of myeloid dendritic cell cytokine production / embryonic morphogenesis / protein methyltransferase activity / vinculin binding / poly(A) binding / exonuclease activity / tRNA processing in the nucleus / regulation of translational initiation / IRE1-mediated unfolded protein response / spliceosomal complex assembly / RNA polymerase II complex binding / negative regulation of protein kinase activity / catalytic complex / bioluminescence / generation of precursor metabolites and energy / mitotic spindle / transcription coregulator activity / cytoplasmic stress granule / double-strand break repair / nuclear envelope / double-stranded RNA binding / defense response to virus / innate immune response / positive regulation of canonical NF-kappaB signal transduction / RNA helicase activity / RNA helicase / ribonucleoprotein complex / centrosome / chromatin binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA-templated transcription / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
FAM98 / Ashwin / Protein of unknown function (DUF2465) / Developmental protein / RNA transcription, translation and transport factor protein / RNA transcription, translation and transport factor protein / RNA-splicing ligase RtcB homologue, eukaryotic / Uncharacterized protein family UPF0027 signature. / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily ...FAM98 / Ashwin / Protein of unknown function (DUF2465) / Developmental protein / RNA transcription, translation and transport factor protein / RNA transcription, translation and transport factor protein / RNA-splicing ligase RtcB homologue, eukaryotic / Uncharacterized protein family UPF0027 signature. / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Green fluorescent protein, GFP / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Concanavalin A-like lectin/glucanase domain superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Green fluorescent protein / tRNA-splicing ligase complex subunit FAM98B / ATP-dependent RNA helicase DDX1 / tRNA-splicing ligase complex subunit ASW / tRNA-splicing ligase complex subunit RTRAF / RNA-splicing ligase RTCB
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPfleiderer MM / Jinek M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMPFP3_210571 Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Structural framework for the assembly of the human tRNA ligase complex.
Authors: Moritz M Pfleiderer / Moritz Kleinwächter / Ajse S Nievergelt / Franziska M Boneberg / Alena Kroupova / Javier Martinez / Martin Jinek /
Abstract: In human cells, a subset of tRNA-encoding genes contain introns. These are removed by a spliceosome-independent pathway in which the tRNA splicing endonuclease complex catalyzes intron excision. The ...In human cells, a subset of tRNA-encoding genes contain introns. These are removed by a spliceosome-independent pathway in which the tRNA splicing endonuclease complex catalyzes intron excision. The resulting exons are subsequently ligated by the tRNA-ligase complex (tRNA-LC), comprising Ashwin, CGI-99, FAM98B, DDX1, and RTCB/HSPC117. The molecular architecture and functions of its non-catalytic subunits remain poorly understood. Using cryo-EM, we determined an atomic-resolution structure of human tRNA-LC. CGI-99, DDX1, and FAM98B form an α-helical bundle that contacts RTCB opposite its active site and anchors DDX1 via its C-terminal helix. FAM98B and CGI-99 form an extensively co-folded heterodimer that clamps Ashwin in a pincer-like structure. Structure-based mutagenesis supports the architecture of the complex. We further show that FAM98A and FAM98C assemble distinct RTCB-containing complexes lacking Ashwin, suggesting specialized cellular functions. Our results provide insights into the molecular assembly of the tRNA ligase complex, highlighting its functions in tRNA biogenesis and beyond.
History
DepositionJun 2, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58360.png

Downloads & links

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Map

FileDownload / File: emd_58360.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.37571177 - 0.6161696
Average (Standard dev.)0.00007718268 (±0.011483565)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 233.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58360_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_58360_half_map_1.map
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Half map: #1

Fileemd_58360_half_map_2.map
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Sample components

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Entire : tRNA ligase complex

EntireName: tRNA ligase complex
Components
  • Complex: tRNA ligase complex
    • Protein or peptide: Ashwin
    • Protein or peptide: Protein FAM98B
    • Protein or peptide: RNA transcription, translation and transport factor protein
    • Protein or peptide: ATP-dependent RNA helicase DDX1,Green fluorescent protein
    • Protein or peptide: RNA-splicing ligase RtcB homolog
  • Ligand: MAGNESIUM ION

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Supramolecule #1: tRNA ligase complex

SupramoleculeName: tRNA ligase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ashwin

MacromoleculeName: Ashwin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.940758 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG SGWSHPQFEK PPSGADPMAG DVGGRSCTDS ELLLHPELLS QEFLLLTLEQ KNIAVETDVR VNKDSLTDLY VQHAIPLPQ RDLPKNRWGK MMEKKREQHE IKNETKRSST VDGLRKRPLI VFDGSSTSTS IKVKKTENGD NDRLKPPPQA S FTSNAFRK ...String:
MWSHPQFEKG SGWSHPQFEK PPSGADPMAG DVGGRSCTDS ELLLHPELLS QEFLLLTLEQ KNIAVETDVR VNKDSLTDLY VQHAIPLPQ RDLPKNRWGK MMEKKREQHE IKNETKRSST VDGLRKRPLI VFDGSSTSTS IKVKKTENGD NDRLKPPPQA S FTSNAFRK LSNSSSSVSP LILSSNLPVN NKTEHNNNDA KQNHDLTHRK SPSGPVKSPP LSPVGTTPVK LKRAAPKEEA EA MNNLKPP QAKRKIQHVT WP

UniProtKB: tRNA-splicing ligase complex subunit ASW

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Macromolecule #2: Protein FAM98B

MacromoleculeName: Protein FAM98B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.153664 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRGPEPGPQP TMEGDVLDTL EALGYKGPLL EEQALTKAAE GGLSSPEFSE LCIWLGSQIK SLCNLEESIT SAGRDDLESF QLEISGFLK EMACPYSVLI SGDIKDRLKK KEDCLKLLLF LSTELQASQI LQNKKHKNSQ LDKNSEVYQE VQAMFDTLGI P KSTTSDIP ...String:
MRGPEPGPQP TMEGDVLDTL EALGYKGPLL EEQALTKAAE GGLSSPEFSE LCIWLGSQIK SLCNLEESIT SAGRDDLESF QLEISGFLK EMACPYSVLI SGDIKDRLKK KEDCLKLLLF LSTELQASQI LQNKKHKNSQ LDKNSEVYQE VQAMFDTLGI P KSTTSDIP HMLNQVESKV KDILSKVQKN HVGKPLLKMD LNSEQAEQLE RINDALSCEY ECRRRMLMKR LDVTVQSFGW SD RAKVKTD DIARIYQPKR YALSPKTTIT MAHLLAARED LSKIIRTSSG TSREKTACAI NKVLMGRVPD RGGRPNEIEP PPP EMPPWQ KRQE

UniProtKB: tRNA-splicing ligase complex subunit FAM98B

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Macromolecule #3: RNA transcription, translation and transport factor protein

MacromoleculeName: RNA transcription, translation and transport factor protein
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.110115 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFRRKLTALD YHNPAGFNCK DETEFRNFIV WLEDQKIRHY KIEDRGNLRN IHSSDWPKFF EKYLRDVNCP FKIQDRQEAI DWLLGLAVR LEYGDNAEKY KDLVPDNSKT ADNATKNAEP LINLDVNNPD FKAGVMALAN LLQIQRHDDY LVMLKAIRIL V QERLTQDA ...String:
MFRRKLTALD YHNPAGFNCK DETEFRNFIV WLEDQKIRHY KIEDRGNLRN IHSSDWPKFF EKYLRDVNCP FKIQDRQEAI DWLLGLAVR LEYGDNAEKY KDLVPDNSKT ADNATKNAEP LINLDVNNPD FKAGVMALAN LLQIQRHDDY LVMLKAIRIL V QERLTQDA VAKANQTKEG LPVALDKHIL GFDTGDAVLN EAAQILRLLH IEELRELQTK INEAIVAVQA IIADPKTDHR LG KVGR

UniProtKB: tRNA-splicing ligase complex subunit RTRAF

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Macromolecule #4: ATP-dependent RNA helicase DDX1,Green fluorescent protein

MacromoleculeName: ATP-dependent RNA helicase DDX1,Green fluorescent protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 36.400836 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGGGSYKGHV DILAPTVQEL AALEKEAQTS FLHLGYLPNQ LFRTFSFGSG ATNFSLLKQA GDVEENPGPG SGEGRGSLLT CGDVEENPG PMVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTLTYGV Q CFSRYPDH ...String:
MGGGSYKGHV DILAPTVQEL AALEKEAQTS FLHLGYLPNQ LFRTFSFGSG ATNFSLLKQA GDVEENPGPG SGEGRGSLLT CGDVEENPG PMVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTLTYGV Q CFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNYNS HN VYIMADK HKNGIKVNFK IRHNIEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSTQSK LSKDPNEKRD HMVLLEFVTA AGI TLGMDE LYK

UniProtKB: ATP-dependent RNA helicase DDX1, Green fluorescent protein

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Macromolecule #5: RNA-splicing ligase RtcB homolog

MacromoleculeName: RNA-splicing ligase RtcB homolog / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: 3'-phosphate/5'-hydroxy nucleic acid ligase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.142207 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHP PSGADPMSRS YNDELQFLEK INKNCWRIKK GFVPNMQVEG VFYVNDALEK LMFEELRNAC RGGGVGGFLP AMKQIGNVA ALPGIVHRSI GLPDVHSGYG FAIGNMAAFD MNDPEAVVSP GGVGFDINCG VRLLRTNLDE SDVQPVKEQL A QAMFDHIP ...String:
MHHHHHHHHP PSGADPMSRS YNDELQFLEK INKNCWRIKK GFVPNMQVEG VFYVNDALEK LMFEELRNAC RGGGVGGFLP AMKQIGNVA ALPGIVHRSI GLPDVHSGYG FAIGNMAAFD MNDPEAVVSP GGVGFDINCG VRLLRTNLDE SDVQPVKEQL A QAMFDHIP VGVGSKGVIP MNAKDLEEAL EMGVDWSLRE GYAWAEDKEH CEEYGRMLQA DPNKVSARAK KRGLPQLGTL GA GNHYAEI QVVDEIFNEY AAKKMGIDHK GQVCVMIHSG SRGLGHQVAT DALVAMEKAM KRDKIIVNDR QLACARIASP EGQ DYLKGM AAAGNYAWVN RSSMTFLTRQ AFAKVFNTTP DDLDLHVIYD VSHNIAKVEQ HVVDGKERTL LVHRKGSTRA FPPH HPLIA VDYQLTGQPV LIGGTMGTCS YVLTGTEQGM TETFGTTCHG AGRALSRAKS RRNLDFQDVL DKLADMGIAI RVASP KLVM EEAPESYKNV TDVVNTCHDA GISKKAIKLR PIAVIKG

UniProtKB: RNA-splicing ligase RTCB

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 291506
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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