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- EMDB-16976: Human tRNA guanine transglycosylase (TGT) bound to tRNAAsp -

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Basic information

Entry
Database: EMDB / ID: EMD-16976
TitleHuman tRNA guanine transglycosylase (TGT) bound to tRNAAsp
Map data
Sample
  • Complex: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
    • Protein or peptide: Queuine tRNA-ribosyltransferase catalytic subunit 1
    • Protein or peptide: Queuine tRNA-ribosyltransferase accessory subunit 2
    • RNA: tRNAAsp
  • Ligand: ZINC ION
  • Ligand: 9-DEAZAGUANINE
KeywordsRNA modification / transglycosylation / nucleid acid-protein complex / tRNA binding / RNA BINDING PROTEIN
Function / homology
Function and homology information


tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity ...tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion / 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 catalytic subunit 1 / Queuine tRNA-ribosyltransferase accessory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSievers K / Neumann P / Susac L / Trowitzsch S / Tampe R / Ficner R
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Structure / Year: 2024
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
DepositionMar 31, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16976.png

Downloads & links

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Map

FileDownload / File: emd_16976.map.gz / Format: CCP4 / Size: 71.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.78 Å
Density
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-0.54850495 - 1.1693897
Average (Standard dev.)-0.0003401108 (±0.035405926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions266266266
Spacing266266266
CellA=B=C: 207.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16976_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16976_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16976_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Ternary complex of human tRNA guanine transglycosylase and tRNAAsp

EntireName: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
Components
  • Complex: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
    • Protein or peptide: Queuine tRNA-ribosyltransferase catalytic subunit 1
    • Protein or peptide: Queuine tRNA-ribosyltransferase accessory subunit 2
    • RNA: tRNAAsp
  • Ligand: ZINC ION
  • Ligand: 9-DEAZAGUANINE

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Supramolecule #1: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp

SupramoleculeName: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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 / Details: Zn ion and 9DG are ligands / Number of copies: 1 / Enantiomer: LEVO / EC number: tRNA-guanosine34 preQ1 transglycosylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.25177 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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 / Details: Zn is an ion / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.77568 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: tRNAAsp

MacromoleculeName: tRNAAsp / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.148312 KDa
SequenceString:
AGGUCGUUAG UAUAGUGGUG AGUAUCCCCG CCUGUCACGC GGGAGACCGG GGUUCGAUUC CCCGACGGCC UGCCA

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: 9-DEAZAGUANINE

MacromoleculeName: 9-DEAZAGUANINE / type: ligand / ID: 5 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Image recordingFilm 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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7nq4

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 463140
FSC plot (resolution estimation)

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