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- EMDB-55078: minimal tRNA ligase complex bound by PYROXD1 -

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Basic information

Entry
Database: EMDB / ID: EMD-55078
Titleminimal tRNA ligase complex bound by PYROXD1
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: Glutathione S-transferase class-mu 26 kDa isozyme,tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1
    • Protein or peptide: RNA-splicing ligase RtcB homolog
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
  • Ligand: MAGNESIUM ION
KeywordsProtein complex / ligase / helicase
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 / NADPH dehydrogenase / tRNA splicing, via endonucleolytic cleavage and ligation ...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 / NADPH dehydrogenase / tRNA splicing, via endonucleolytic cleavage and ligation / protein localization to cytoplasmic stress granule / molecular sensor activity / RNA transport / NAD(P)H oxidase H2O2-forming activity / NADPH dehydrogenase activity / 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 / glutathione transferase / RNA polymerase II complex binding / NADH dehydrogenase activity / glutathione transferase activity / negative regulation of protein kinase activity / catalytic complex / bioluminescence / glutathione metabolic process / sarcomere / 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 / cellular response to oxidative stress / 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
NADH-rubredoxin oxidoreductase, C-terminal / Rubredoxin NAD+ reductase C-terminal domain / 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. ...NADH-rubredoxin oxidoreductase, C-terminal / Rubredoxin NAD+ reductase C-terminal domain / 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 / : / Glutathione S-transferase, C-terminal domain / : / RNA helicase, DEAD-box type, Q motif / FAD/NAD-linked reductase, dimerisation domain superfamily / DEAD-box RNA helicase Q motif profile. / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / 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 / Glutathione S-transferase, C-terminal domain superfamily / Green fluorescent protein, GFP / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / FAD/NAD(P)-binding domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Concanavalin A-like lectin/glucanase domain superfamily / Thioredoxin-like 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
Glutathione S-transferase class-mu 26 kDa isozyme / Green fluorescent protein / tRNA-splicing ligase complex subunit FAM98B / tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1 / 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: 3.25 Å
AuthorsPfleiderer MM / Jinek M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMPFP3_210571 Switzerland
CitationJournal: To Be Published
Title: Molecular architecture of the tRNA ligation complex
Authors: Pfleiderer MM / Leitner M / Pascarelli S / Nievergelt AS / Martinez J / Jinek M
History
DepositionSep 16, 2025-
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_55078.png

Downloads & links

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Map

FileDownload / File: emd_55078.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.37240744 - 0.52009416
Average (Standard dev.)-0.00011995731 (±0.015028872)
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_55078_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55078_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55078_half_map_2.map
Projections & Slices
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Histogram (log scale)

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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: Glutathione S-transferase class-mu 26 kDa isozyme,tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1
    • Protein or peptide: RNA-splicing ligase RtcB homolog
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
  • 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-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 158 KDa

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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: Glutathione S-transferase class-mu 26 kDa isozyme,tRNA ligase com...

MacromoleculeName: Glutathione S-transferase class-mu 26 kDa isozyme,tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: glutathione transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.722938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM CLDAFPKLVC FKKRIEAIPQ IDKYLKSSKY IAWPLQGWQA TFGGGDHPPK SDLEVLFQGP LGSMEAARPP PT AGKFVVV GGGIAGVTCA EQLATHFPSE DILLVTASPV IKAVTNFKQI SKILEEFDVE EQSSTMLGKR FPNIKVIESG VKQ LKSEEH CIVTEDGNQH VYKKLCLCAG AKPKLICEGN PYVLGIRDTD SAQEFQKQLT KAKRIMIIGN GGIALELVYE IEGC EVIWA IKDKAIGNTF FDAGAAEFLT SKLIAEKSEA KIAHKRTRYT TEGRKKEARS KSKADNVGSA LGPDWHEGLN LKGTK EFSH KIHLETMCEV KKIYLQDEFR ILKKKSFTFP RDHKSVTADT EMWPVYVELT NEKIYGCDFI VSATGVTPNV EPFLHG NSF DLGEDGGLKV DDHMHTSLPD IYAAGDICTT SWQLSPVWQQ MRLWTQARQM GWYAAKCMAA ASSGDSIDMD FSFELFA HV TKFFNYKVVL LGKYNAQGLG SDHELMLRCT KGREYIKVVM QNGRMMGAVL IGETDLEETF ENLILNQMNL SSYGEDLL D PNIDIEDYFD

UniProtKB: Glutathione S-transferase class-mu 26 kDa isozyme, tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1

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Macromolecule #6: RNA-splicing ligase RtcB homolog

MacromoleculeName: RNA-splicing ligase RtcB homolog / type: protein_or_peptide / ID: 6 / 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 #7: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 7 / Number of copies: 1 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #8: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE

MacromoleculeName: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / type: ligand / ID: 8 / Number of copies: 1 / Formula: FDA
Molecular weightTheoretical: 787.566 Da
Chemical component information

ChemComp-FDA:
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 2 / 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
Component:
ConcentrationFormulaName
150.0 mMKClPotassium chloride
20.0 mMHEPESHEPES
10.0 mMdesthiobiotin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / 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: 2.6 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: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 269780
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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