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- PDB-31fw: Human tRNA ligase complex -

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Basic information

Entry
Database: PDB / ID: 31fw
TitleHuman tRNA ligase complex
Components
  • ATP-dependent RNA helicase DDX1,Green fluorescent protein
  • Ashwin
  • Protein FAM98B
  • RNA transcription, translation and transport factor protein
  • RNA-splicing ligase RtcB homolog
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPfleiderer, M.M. / Jinek, M.
Funding support Switzerland, 1items
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, 2026Deposition 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
R: RNA-splicing ligase RtcB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,7726
Polymers187,7485
Non-polymers241
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 , 5 types, 5 molecules ABCDR

#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 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 , 1 types, 1 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291506 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027663
ELECTRON MICROSCOPYf_angle_d0.53410329
ELECTRON MICROSCOPYf_dihedral_angle_d4.4581019
ELECTRON MICROSCOPYf_chiral_restr0.041167
ELECTRON MICROSCOPYf_plane_restr0.0031329

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