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Open data
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Basic information
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Title | Human tRNA guanine transglycosylase (TGT) bound to tRNAAsp | |||||||||
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Function / homology | ![]() tRNA-guanosine34 queuine transglycosylase / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Sievers K / Neumann P / Susac L / Trowitzsch S / Tampe R / Ficner R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase. Authors: Katharina Sievers / Piotr Neumann / Lukas Sušac / Stefano Da Vela / Melissa Graewert / Simon Trowitzsch / Dmitri Svergun / Robert Tampé / Ralf Ficner / ![]() Abstract: Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine ...Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 35.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.3 KB 17.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.5 KB | Display | ![]() |
Images | ![]() | 100.1 KB | ||
Masks | ![]() | 71.8 MB | ![]() | |
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 66.8 MB 66.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8omrMC M: atomic model generated by this map C: citing same article ( |
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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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Voxel size | X=Y=Z: 0.78 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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-Half map: #2
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Density Histograms |
-Half map: #1
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Sample components
-Entire : Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
Entire | Name: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp |
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Components |
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-Supramolecule #1: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
Supramolecule | Name: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Queuine tRNA-ribosyltransferase catalytic subunit 1
Macromolecule | Name: Queuine tRNA-ribosyltransferase catalytic subunit 1 / type: protein_or_peptide / ID: 1 / Details: Zn ion and 9DG are ligands / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-guanosine34 preQ1 transglycosylase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 44.25177 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GPMAGAATQA SLESAPRIMR LVAECSRSRA RAGELWLPHG TVATPVFMPV GTQATMKGIT TEQLDALGCR ICLGNTYHLG LRPGPELIQ KANGLHGFMN WPHNLLTDSG GFQMVSLVSL SEVTEEGVRF RSPYDGNETL LSPEKSVQIQ NALGSDIIMQ L DDVVSSTV ...String: GPMAGAATQA SLESAPRIMR LVAECSRSRA RAGELWLPHG TVATPVFMPV GTQATMKGIT TEQLDALGCR ICLGNTYHLG LRPGPELIQ KANGLHGFMN WPHNLLTDSG GFQMVSLVSL SEVTEEGVRF RSPYDGNETL LSPEKSVQIQ NALGSDIIMQ L DDVVSSTV TGPRVEEAMY RSIRWLDRCI AAHQRPDKQN LFAIIQGGLD ADLRATCLEE MTKRDVPGFA IGGLSGGESK SQ FWRMVAL STSRLPKDKP RYLMGVGYAT DLVVCVALGC DMFDCVFPTR TARFGSALVP TGNLQLRKKV FEKDFGPIDP ECT CPTCQK HSRAFLHALL HSDNTAALHH LTVHNIAYQL QLMSAVRTSI VEKRFPDFVR DFMGAMYGDP TLCPTWATDA LASV GITLG 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 / Details: Zn is an ion / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.77568 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MKLSLTKVVN GCRLGKIKNL GKTGDHTMDI PGCLLYTKTG SAPHLTHHTL HNIHGVPAMA QLTLSSLAEH HEVLTEYKEG VGKFIGMPE SLLYCSLHDP VSPCPAGYVT NKSVSVWSVA GRVEMTVSKF MAIQKALQPD WFQCLSDGEV SCKEATSIKR V RKSVDRSL ...String: MKLSLTKVVN GCRLGKIKNL GKTGDHTMDI PGCLLYTKTG SAPHLTHHTL HNIHGVPAMA QLTLSSLAEH HEVLTEYKEG VGKFIGMPE SLLYCSLHDP VSPCPAGYVT NKSVSVWSVA GRVEMTVSKF MAIQKALQPD WFQCLSDGEV SCKEATSIKR V RKSVDRSL LFLDNCLRLQ EESEVLQKSV IIGVIEGGDV MEERLRSARE TAKRPVGGFL LDGFQGNPTT LEARLRLLSS VT AELPEDK PRLISGVSRP DEVLECIERG VDLFESFFPY QVTERGCALT FSFDYQPNPE ETLLQQNGTQ EEIKCMDQIK KIE TTGCNQ EITSFEINLK EKKYQEDFNP LVRGCSCYCC KNHTRAYIHH LLVTNELLAG VLLMMHNFEH YFGFFHYIRE ALKS DKLAQ LKELIHRQAS UniProtKB: Queuine tRNA-ribosyltransferase accessory subunit 2 |
-Macromolecule #3: tRNAAsp
Macromolecule | Name: tRNAAsp / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.148312 KDa |
Sequence | String: AGGUCGUUAG UAUAGUGGUG AGUAUCCCCG CCUGUCACGC GGGAGACCGG GGUUCGAUUC CCCGACGGCC UGCCA |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: 9-DEAZAGUANINE
Macromolecule | Name: 9-DEAZAGUANINE / type: ligand / ID: 5 / 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 | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 44.46 sec. / Average electron dose: 62.1 e/Å2 |