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- PDB-9spe: Human tRNA ligase complex bound by PYROXD1 -

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Basic information

Entry
Database: PDB / ID: 9spe
TitleHuman tRNA ligase complex bound by PYROXD1
Components
  • ATP-dependent RNA helicase DDX1,Green fluorescent protein
  • Ashwin
  • Glutathione S-transferase class-mu 26 kDa isozyme,tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1
  • Protein FAM98B
  • RNA transcription, translation and transport factor protein
  • RNA-splicing ligase RtcB homolog
KeywordsLIGASE / Protein complex / 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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)
Schistosoma japonicum (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsPfleiderer, M.M. / Jinek, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationTMPFP3_210571 Switzerland
CitationJournal: To Be Published
Title: Molecular architecture of the tRNA ligation complex
Authors: Pfleiderer, M.M. / Leitner, M. / Pascarelli, S. / Nievergelt, A.S. / Martinez, J. / Jinek, M.
History
DepositionSep 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ashwin
B: Protein FAM98B
C: RNA transcription, translation and transport factor protein
D: ATP-dependent RNA helicase DDX1,Green fluorescent protein
P: Glutathione S-transferase class-mu 26 kDa isozyme,tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1
R: RNA-splicing ligase RtcB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,97010
Polymers270,4716
Non-polymers1,5004
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 6 molecules ABCDPR

#1: Protein Ashwin


Mass: 28940.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C2orf49 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BVC5
#2: Protein Protein FAM98B


Mass: 37153.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM98B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q52LJ0
#3: Protein RNA transcription, translation and transport factor protein / CLE7 homolog / CLE / hCLE


Mass: 28110.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTRAF, C14orf166, CGI-99 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y224
#4: Protein ATP-dependent RNA helicase DDX1,Green fluorescent protein / DEAD box protein 1 / DEAD box protein retinoblastoma / DBP-RB


Mass: 36400.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish)
Gene: DDX1, GFP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92499, UniProt: P42212, RNA helicase
#5: Protein Glutathione S-transferase class-mu 26 kDa isozyme,tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1 / GST 26 / Sj26 antigen / SjGST / Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1


Mass: 82722.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Homo sapiens (human)
Gene: PYROXD1 / Production host: Escherichia coli (E. coli)
References: UniProt: P08515, UniProt: Q8WU10, glutathione transferase, NADPH dehydrogenase
#6: Protein RNA-splicing ligase RtcB homolog / 3'-phosphate/5'-hydroxy nucleic acid ligase


Mass: 57142.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTCB, C22orf28, HSPC117 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y3I0, 3'-phosphate/5'-hydroxy nucleic acid ligase

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Non-polymers , 3 types, 4 molecules

#7: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#8: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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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: tRNA-ligase complex / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 0.158 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera (butterflies/moths)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMPotassium chlorideKCl1
220 mMHEPESHEPES1
310 mMdesthiobiotin1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 269780 / Symmetry type: POINT
RefinementHighest resolution: 3.25 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311431
ELECTRON MICROSCOPYf_angle_d0.57515436
ELECTRON MICROSCOPYf_dihedral_angle_d7.3811624
ELECTRON MICROSCOPYf_chiral_restr0.0431724
ELECTRON MICROSCOPYf_plane_restr0.0041974

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