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

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Basic information

Entry
Database: PDB / ID: 9hn9
TitleMouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4
Components
  • Queuine tRNA-ribosyltransferase accessory subunit 2
  • Queuine tRNA-ribosyltransferase catalytic subunit 1
  • mouse pre-tRNA-Tyr-1-4
KeywordsRNA BINDING PROTEIN / queuosine / tRNA / QTRT1/2 / tRNA modification
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
9-DEAZAGUANINE / RNA / RNA (> 10) / Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase catalytic subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKaczmarczyk, I. / Koziej, L. / Glatt, S.
Funding supportEuropean Union, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase catalytic subunit 1
B: Queuine tRNA-ribosyltransferase accessory subunit 2
C: mouse pre-tRNA-Tyr-1-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9484
Polymers119,7983
Non-polymers1501
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Queuine tRNA-ribosyltransferase catalytic subunit 1 / Guanine insertion enzyme / tRNA-guanine transglycosylase


Mass: 43428.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt1, Tgt, Tgut / Production host: Vibrio natriegens (bacteria)
References: UniProt: Q9JMA2, tRNA-guanosine34 preQ1 transglycosylase
#2: Protein Queuine tRNA-ribosyltransferase accessory subunit 2 / Queuine tRNA-ribosyltransferase domain-containing protein 1


Mass: 46367.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt2, Qtrtd1 / Production host: Vibrio natriegens (bacteria) / References: UniProt: B8ZXI1
#3: RNA chain mouse pre-tRNA-Tyr-1-4


Mass: 30001.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Chemical ChemComp-9DG / 9-DEAZAGUANINE


Mass: 150.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4O / Feature type: SUBJECT OF INVESTIGATION
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: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Vibrio natriegens (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2100 mMsodium chlorideNaCl1
31 mMmagnesium chlorideMgCl21
42 mMdithiothreitolDTT1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
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 / Calibrated magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.82 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9687
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.3particle selection
2EPU2.10.0.1941RELimage acquisition
4cryoSPARC4.5.3CTF correction
7ISOLDE1.7.1model fitting
8UCSF ChimeraX1.7.1model fitting
10cryoSPARC4.5.3initial Euler assignmentAb-initio
11RELION5.0-betafinal Euler assignment3D auto-refine
12RELION5.0-betaclassification3D classification
13RELION5.0-beta3D reconstruction3D auto-refine
14PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1933554 / Details: Template picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 396050 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Isolde
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDChain residue rangeDetailsInitial refinement model-IDPdb chain residue rangeSource nameType
17OV9

7ov9

A7OV9A2-414QTRT212-414PDBexperimental model
27OV9

7ov9

C7OV9C12-402QTRT1112-402PDBexperimental model
3mouse pre-tRNA-Tyr-1-4AlphaFoldin silico model
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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