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- EMDB-52309: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4 -

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Basic information

Entry
Database: EMDB / ID: EMD-52309
TitleMouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4
Map dataMap combined from 2 independent halves. Not post-processed.
Sample
  • Complex: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4
    • Protein or peptide: Queuine tRNA-ribosyltransferase catalytic subunit 1
    • Protein or peptide: Queuine tRNA-ribosyltransferase accessory subunit 2
    • RNA: mouse pre-tRNA-Tyr-1-4
  • Ligand: 9-DEAZAGUANINE
Keywordsqueuosine / tRNA / QTRT1/2 / tRNA modification / RNA BINDING PROTEIN
Function / homology
Function and homology information


tRNA-guanosine34 queuine transglycosylase / tRNA-guanine transglycosylase complex / cytoplasmic side of mitochondrial outer membrane / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion ...tRNA-guanosine34 queuine transglycosylase / tRNA-guanine transglycosylase complex / cytoplasmic side of mitochondrial outer membrane / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Queuine tRNA-ribosyltransferase accessory subunit QTRTD1 / : / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase catalytic subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKaczmarczyk I / Koziej L / Glatt S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101001394European Union
CitationJournal: Nat Commun / Year: 2025
Title: Queuosine is incorporated into precursor tRNA before splicing.
Authors: Wei Guo / Igor Kaczmarczyk / Kevin Kopietz / Florian Flegler / Stefano Russo / Ege Cigirgan / Andrzej Chramiec-Głąbik / Łukasz Koziej / Cansu Cirzi / Jirka Peschek / Klaus Reuter / Mark ...Authors: Wei Guo / Igor Kaczmarczyk / Kevin Kopietz / Florian Flegler / Stefano Russo / Ege Cigirgan / Andrzej Chramiec-Głąbik / Łukasz Koziej / Cansu Cirzi / Jirka Peschek / Klaus Reuter / Mark Helm / Sebastian Glatt / Francesca Tuorto /
Abstract: Each newly transcribed tRNA molecule must undergo processing and receive modifications to become functional. Queuosine (Q) is a tRNA modification present at position 34 of four tRNAs with "GUN" ...Each newly transcribed tRNA molecule must undergo processing and receive modifications to become functional. Queuosine (Q) is a tRNA modification present at position 34 of four tRNAs with "GUN" anticodons. Among these, the precursor of tRNA carries an intronic sequence within the anticodon loop that is removed by an essential non-canonical splicing event. The functional and temporal coupling between tRNA-splicing and Q-incorporation remains elusive. Here, we demonstrate in vitro and in vivo that intron-containing precursors of tRNA are modified with Q or with the Q-derivative galactosyl-queuosine (galQ) before being spliced. We show that this order of events is conserved in mouse, human, flies and worms. Using single particle cryo-EM, we confirm that pre-tRNA is a bona fide substrate of the QTRT1/2 complex, which catalyzes the incorporation of Q into the tRNA. Our results elucidate the hierarchical interplay that coordinates Q-incorporation and splicing in eukaryotic tRNAs, providing a relevant but unappreciated aspect of the cellular tRNA maturation process.
History
DepositionDec 10, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_52309.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap combined from 2 independent halves. Not post-processed.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 252. Å
0.84 Å/pix.
x 300 pix.
= 252. Å
0.84 Å/pix.
x 300 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0033283003 - 0.007930754
Average (Standard dev.)0.0000048119264 (±0.00016118617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52309_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Combined half maps post-processed using sharpening B factor 119.

Fileemd_52309_additional_1.map
AnnotationCombined half maps post-processed using sharpening B factor 119.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_52309_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_52309_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4

EntireName: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4
Components
  • Complex: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4
    • Protein or peptide: Queuine tRNA-ribosyltransferase catalytic subunit 1
    • Protein or peptide: Queuine tRNA-ribosyltransferase accessory subunit 2
    • RNA: mouse pre-tRNA-Tyr-1-4
  • Ligand: 9-DEAZAGUANINE

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Supramolecule #1: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4

SupramoleculeName: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Queuine tRNA-ribosyltransferase catalytic subunit 1

MacromoleculeName: Queuine tRNA-ribosyltransferase catalytic subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-guanosine34 preQ1 transglycosylase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 43.42898 KDa
Recombinant expressionOrganism: Vibrio natriegens (bacteria)
SequenceString: GPESAPRIMR LVAECSRSGA RAGELRLPHG TVATPVFMPV GTQATMKGIT TEQLDSLGCR ICLGNTYHLG LRPGPELIRK AQGLHGFMN WPHNLLTDSG GFQMVSLFSL SEVTEEGVHF RSPYDGEETL LSPERSVEIQ NALGSDIIMQ LDHVVSSTVT G PLVEEAMH ...String:
GPESAPRIMR LVAECSRSGA RAGELRLPHG TVATPVFMPV GTQATMKGIT TEQLDSLGCR ICLGNTYHLG LRPGPELIRK AQGLHGFMN WPHNLLTDSG GFQMVSLFSL SEVTEEGVHF RSPYDGEETL LSPERSVEIQ NALGSDIIMQ LDHVVSSTVT G PLVEEAMH RSVRWLDRCI AAHKHPDKQN LFAIIQGGLN ADLRTTCLKE MTKRDVPGFA IGGLSGGESK AQFWKMVALS TS MLPKDKP RYLMGVGYAT DLVVCVALGC DMFDCVYPTR TARFGSALVP TGNLQLKKKQ YAKDFSPINP ECPCPTCQTH SRA FLHALL HSDNTTALHH LTVHNIAYQL QLLSAVRSSI LEQRFPDFVR NFMRTMYGDH SLCPAWAVEA LASVGIMLT

UniProtKB: Queuine tRNA-ribosyltransferase catalytic subunit 1

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Macromolecule #2: Queuine tRNA-ribosyltransferase accessory subunit 2

MacromoleculeName: Queuine tRNA-ribosyltransferase accessory subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 46.367172 KDa
Recombinant expressionOrganism: Vibrio natriegens (bacteria)
SequenceString: GPKLSLIKVV NGCRLGKIQN LGKAGDCTVD IPGCLLYTRT GSAPHLTHQT LRNIHGVPGI AQLTLSSLAE HHEVLAEYKK GVGSFIGMP ESLFYCSLHD PVTPGPAGYV TSKSVSVWGF GGRVEMTVSK FMAIQEALQP DWFQCLSDGE ASCAETTSIK R ARKSVDRS ...String:
GPKLSLIKVV NGCRLGKIQN LGKAGDCTVD IPGCLLYTRT GSAPHLTHQT LRNIHGVPGI AQLTLSSLAE HHEVLAEYKK GVGSFIGMP ESLFYCSLHD PVTPGPAGYV TSKSVSVWGF GGRVEMTVSK FMAIQEALQP DWFQCLSDGE ASCAETTSIK R ARKSVDRS LLFLDSCLRL QEESEVLQKS VIIGVIEGGD VMEERLRSAR ETAKRPVGGF LLDGFQGDPA VTETRLHLLS SV TAELPED KPRLICGVSR PDEVLECIER GVDLFESFFP YQVTERGCAL TFTFDCQLNP EETLLQQNGI QEKIKGLDQA KKI EATGCN QEMTSFEINL KEKKYQEDFD PLVRGCSCYC CKNHTRAYIH HLLMTNELLA GVLLMMHNFE HYFGFFCSIR EALK NDTLA QLKELICRQM F

UniProtKB: Queuine tRNA-ribosyltransferase accessory subunit 2

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Macromolecule #3: mouse pre-tRNA-Tyr-1-4

MacromoleculeName: mouse pre-tRNA-Tyr-1-4 / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 30.00174 KDa
SequenceString:
GGCCUUCGAU AGCUCAGUUG GUAGAGCGGA GGACUGUAGG UCAUUGUUCU AGAAAUCCUU AGGUCGCUGG UUCGAAUCCG GCUCGAAGG ACCA

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Macromolecule #4: 9-DEAZAGUANINE

MacromoleculeName: 9-DEAZAGUANINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: 9DG
Molecular weightTheoretical: 150.138 Da
Chemical component information

ChemComp-9DG:
9-DEAZAGUANINE

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride
2.0 mMDTTdithiothreitol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 9687 / Average exposure time: 1.82 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1933554 / Details: Template picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta) / Software - details: 3D auto-refine / Number images used: 396050
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta) / Software - details: 3D auto-refine
Final 3D classificationNumber classes: 3 / Avg.num./class: 141418 / Software - Name: RELION (ver. 5.0-beta) / Software - details: 3D classification / Details: Blush regularisation
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

chain_id: A, residue_range: 2-414, source_name: PDB, initial_model_type: experimental modelQTRT2

chain_id: C, residue_range: 12-402, source_name: PDB, initial_model_type: experimental modelQTRT1
source_name: AlphaFold, initial_model_type: in silico modelmouse pre-tRNA-Tyr-1-4
DetailsIsolde
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9hn9:
Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4

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