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- EMDB-55075: DeepEMhancer modified map of the human tNRA ligase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-55075
TitleDeepEMhancer modified map of the human tNRA ligase complex
Map data
Sample
  • Complex: tRNA ligase complex
    • Protein or peptide: Ashwin
    • Protein or peptide: CGI-99
    • Protein or peptide: FAM98B
    • Protein or peptide: DDX1
    • Protein or peptide: HSPC117
KeywordsComplex / Ligase / 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 / 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 / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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
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)
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_55075.png

Downloads & links

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Map

FileDownload / File: emd_55075.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: 0.0981
Minimum - Maximum-0.001808896 - 2.5095098
Average (Standard dev.)0.0013800944 (±0.027194116)
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_55075_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55075_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55075_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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: CGI-99
    • Protein or peptide: FAM98B
    • Protein or peptide: DDX1
    • Protein or peptide: HSPC117

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Supramolecule #1: tRNA ligase complex

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

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Macromolecule #1: Ashwin

MacromoleculeName: Ashwin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG SGWSHPQFEK PPSGADPMAG DVGGRSCTDS ELLLHPELLS QEFLLLTLEQ KNIAVETDVR VNKDSLTDLY VQHAIPLPQR DLPKNRWGKM MEKKREQHEI KNETKRSSTV DGLRKRPLIV FDGSSTSTSI KVKKTENGDN DRLKPPPQAS FTSNAFRKLS ...String:
MWSHPQFEKG SGWSHPQFEK PPSGADPMAG DVGGRSCTDS ELLLHPELLS QEFLLLTLEQ KNIAVETDVR VNKDSLTDLY VQHAIPLPQR DLPKNRWGKM MEKKREQHEI KNETKRSSTV DGLRKRPLIV FDGSSTSTSI KVKKTENGDN DRLKPPPQAS FTSNAFRKLS NSSSSVSPLI LSSNLPVNNK TEHNNNDAKQ NHDLTHRKSP SGPVKSPPLS PVGTTPVKLK RAAPKEEAEA MNNLKPPQAK RKIQHVTWP

UniProtKB: tRNA-splicing ligase complex subunit ASW

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Macromolecule #2: CGI-99

MacromoleculeName: CGI-99 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFRRKLTALD YHNPAGFNCK DETEFRNFIV WLEDQKIRHY KIEDRGNLRN IHSSDWPKFF EKYLRDVNCP FKIQDRQEAI DWLLGLAVRL EYGDNAEKYK DLVPDNSKTA DNATKNAEPL INLDVNNPDF KAGVMALANL LQIQRHDDYL VMLKAIRILV QERLTQDAVA ...String:
MFRRKLTALD YHNPAGFNCK DETEFRNFIV WLEDQKIRHY KIEDRGNLRN IHSSDWPKFF EKYLRDVNCP FKIQDRQEAI DWLLGLAVRL EYGDNAEKYK DLVPDNSKTA DNATKNAEPL INLDVNNPDF KAGVMALANL LQIQRHDDYL VMLKAIRILV QERLTQDAVA KANQTKEGLP VALDKHILGF DTGDAVLNEA AQILRLLHIE ELRELQTKIN EAIVAVQAII ADPKTDHRLG KVGR

UniProtKB: tRNA-splicing ligase complex subunit RTRAF

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Macromolecule #3: FAM98B

MacromoleculeName: FAM98B / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRGPEPGPQP TMEGDVLDTL EALGYKGPLL EEQALTKAAE GGLSSPEFSE LCIWLGSQIK SLCNLEESIT SAGRDDLESF QLEISGFLKE MACPYSVLIS GDIKDRLKKK EDCLKLLLFL STELQASQIL QNKKHKNSQL DKNSEVYQEV QAMFDTLGIP KSTTSDIPHM ...String:
MRGPEPGPQP TMEGDVLDTL EALGYKGPLL EEQALTKAAE GGLSSPEFSE LCIWLGSQIK SLCNLEESIT SAGRDDLESF QLEISGFLKE MACPYSVLIS GDIKDRLKKK EDCLKLLLFL STELQASQIL QNKKHKNSQL DKNSEVYQEV QAMFDTLGIP KSTTSDIPHM LNQVESKVKD ILSKVQKNHV GKPLLKMDLN SEQAEQLERI NDALSCEYEC RRRMLMKRLD VTVQSFGWSD RAKVKTDDIA RIYQPKRYAL SPKTTITMAH LLAAREDLSK IIRTSSGTSR EKTACAINKV LMGRVPDRGG RPNEIEPPPP EMPPWQKRQE

UniProtKB: tRNA-splicing ligase complex subunit FAM98B

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Macromolecule #4: DDX1

MacromoleculeName: DDX1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGGGSYKGHV DILAPTVQEL AALEKEAQTS FLHLGYLPNQ LFRTFSFGSG ATNFSLLKQA GDVEENPGPG SGEGRGSLLT CGDVEENPGP MVSKGEELFT GVVPILVELD GDVNGHKFSV SGEGEGDATY GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK ...String:
MGGGSYKGHV DILAPTVQEL AALEKEAQTS FLHLGYLPNQ LFRTFSFGSG ATNFSLLKQA GDVEENPGPG SGEGRGSLLT CGDVEENPGP MVSKGEELFT GVVPILVELD GDVNGHKFSV SGEGEGDATY GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK QHDFFKSAMP EGYVQERTIF FKDDGNYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNYNSHN VYIMADKHKN GIKVNFKIRH NIEDGSVQLA DHYQQNTPIG DGPVLLPDNH YLSTQSKLSK DPNEKRDHMV LLEFVTAAGI TLGMDELYK

UniProtKB: ATP-dependent RNA helicase DDX1

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Macromolecule #5: HSPC117

MacromoleculeName: HSPC117 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHP PSGADPMSRS YNDELQFLEK INKNCWRIKK GFVPNMQVEG VFYVNDALEK LMFEELRNAC RGGGVGGFLP AMKQIGNVAA LPGIVHRSIG LPDVHSGYGF AIGNMAAFDM NDPEAVVSPG GVGFDINCGV RLLRTNLDES DVQPVKEQLA QAMFDHIPVG ...String:
MHHHHHHHHP PSGADPMSRS YNDELQFLEK INKNCWRIKK GFVPNMQVEG VFYVNDALEK LMFEELRNAC RGGGVGGFLP AMKQIGNVAA LPGIVHRSIG LPDVHSGYGF AIGNMAAFDM NDPEAVVSPG GVGFDINCGV RLLRTNLDES DVQPVKEQLA QAMFDHIPVG VGSKGVIPMN AKDLEEALEM GVDWSLREGY AWAEDKEHCE EYGRMLQADP NKVSARAKKR GLPQLGTLGA GNHYAEIQVV DEIFNEYAAK KMGIDHKGQV CVMIHSGSRG LGHQVATDAL VAMEKAMKRD KIIVNDRQLA CARIASPEGQ DYLKGMAAAG NYAWVNRSSM TFLTRQAFAK VFNTTPDDLD LHVIYDVSHN IAKVEQHVVD GKERTLLVHR KGSTRAFPPH HPLIAVDYQL TGQPVLIGGT MGTCSYVLTG TEQGMTETFG TTCHGAGRAL SRAKSRRNLD FQDVLDKLAD MGIAIRVASP KLVMEEAPES YKNVTDVVNT CHDAGISKKA IKLRPIAVIK G

UniProtKB: RNA-splicing ligase RTCB

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 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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