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Open data
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Basic information
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Title | Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4 | |||||||||
![]() | Map combined from 2 independent halves. Not post-processed. | |||||||||
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![]() | queuosine / tRNA / QTRT1/2 / tRNA modification / RNA BINDING PROTEIN | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Kaczmarczyk I / Koziej L / Glatt S | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 95.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.5 KB 27.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.2 KB | Display | ![]() |
Images | ![]() | 60 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() ![]() | 53.2 MB 81.2 MB 81 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 801.4 KB | Display | ![]() |
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Full document | ![]() | 801 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9hn9MC ![]() 9hn7C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Map combined from 2 independent halves. Not post-processed. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Combined half maps post-processed using sharpening B factor 119.
File | emd_52309_additional_1.map | ||||||||||||
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Annotation | Combined half maps post-processed using sharpening B factor 119. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_52309_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_52309_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4
Entire | Name: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4 |
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Components |
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-Supramolecule #1: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4
Supramolecule | Name: Mouse QTRT1/2 in complex with mouse pre-tRNA-Tyr-1-4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 120 KDa |
-Macromolecule #1: Queuine tRNA-ribosyltransferase catalytic subunit 1
Macromolecule | Name: Queuine tRNA-ribosyltransferase catalytic subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-guanosine34 preQ1 transglycosylase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.42898 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #2: Queuine tRNA-ribosyltransferase accessory subunit 2
Macromolecule | Name: Queuine tRNA-ribosyltransferase accessory subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.367172 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: mouse pre-tRNA-Tyr-1-4
Macromolecule | Name: mouse pre-tRNA-Tyr-1-4 / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 30.00174 KDa |
Sequence | String: GGCCUUCGAU AGCUCAGUUG GUAGAGCGGA GGACUGUAGG UCAUUGUUCU AGAAAUCCUU AGGUCGCUGG UUCGAAUCCG GCUCGAAGG ACCA |
-Macromolecule #4: 9-DEAZAGUANINE
Macromolecule | Name: 9-DEAZAGUANINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: 9DG |
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Molecular weight | Theoretical: 150.138 Da |
Chemical component information | ![]() ChemComp-9DG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: 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 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen 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
-Atomic model buiding 1
Initial model |
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Details | Isolde | ||||||||||||
Refinement | Space: REAL / Protocol: FLEXIBLE FIT | ||||||||||||
Output model | ![]() PDB-9hn9: |