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- EMDB-75125: E. coli TGT covalent intermediate with 1 tRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-75125
TitleE. coli TGT covalent intermediate with 1 tRNA
Map data
Sample
  • Complex: tRNA-transglycosylase covalent intermediate with 1 tRNA
    • Protein or peptide: Queuine tRNA-ribosyltransferase
    • RNA: tRNA(Tyr)
  • Ligand: 9-DEAZAGUANINE
  • Ligand: ZINC ION
KeywordsTGT / RNA modifying enzyme / TRANSFERASE-RNA complex
Function / homology
Function and homology information


tRNA wobble guanine modification / tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA queuosine(34) biosynthetic process / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
: / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsHarjung A / Devaraj N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM141939 United States
CitationJournal: To Be Published
Title: Cryo-EM reveals that tRNA-transglycosylase enzymes from E. coli and Shigella can bind and act upon two tRNAs
Authors: Harjung A / Devaraj N
History
DepositionJan 15, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75125.png

Downloads & links

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Map

FileDownload / File: emd_75125.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.74 Å/pix.
x 256 pix.
= 188.16 Å		0.74 Å/pix.
x 256 pix.
= 188.16 Å		0.74 Å/pix.
x 256 pix.
= 188.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.735 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.41
Minimum - Maximum-13.139734000000001 - 27.721921999999999
Average (Standard dev.)0.000000000010023 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 188.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_75125_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75125_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75125_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : tRNA-transglycosylase covalent intermediate with 1 tRNA

EntireName: tRNA-transglycosylase covalent intermediate with 1 tRNA
Components
  • Complex: tRNA-transglycosylase covalent intermediate with 1 tRNA
    • Protein or peptide: Queuine tRNA-ribosyltransferase
    • RNA: tRNA(Tyr)
  • Ligand: 9-DEAZAGUANINE
  • Ligand: ZINC ION

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Supramolecule #1: tRNA-transglycosylase covalent intermediate with 1 tRNA

SupramoleculeName: tRNA-transglycosylase covalent intermediate with 1 tRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Queuine tRNA-ribosyltransferase

MacromoleculeName: Queuine tRNA-ribosyltransferase / type: protein_or_peptide / ID: 1
Details: MWSHPQFEK: N-terminal Strep-tag HHHHHH: C-terminal His-tag
Number of copies: 2 / Enantiomer: LEVO / EC number: tRNA-guanosine34 preQ1 transglycosylase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.591602 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KGKFELDTTD GRARRGRLVF DRGVVETPCF MPVGTYGTVK GMTPEEVEAT GAQIILGNTF HLWLRPGQEI MKLHGDLHDF MQWKGPILT DSGGFQVFSL GDIRKITEQG VHFRNPINGD PIFLDPEKSM EIQYDLGSDI VMIFDECTPY PADWDYAKRS M EMSLRWAK ...String:
KGKFELDTTD GRARRGRLVF DRGVVETPCF MPVGTYGTVK GMTPEEVEAT GAQIILGNTF HLWLRPGQEI MKLHGDLHDF MQWKGPILT DSGGFQVFSL GDIRKITEQG VHFRNPINGD PIFLDPEKSM EIQYDLGSDI VMIFDECTPY PADWDYAKRS M EMSLRWAK RSRERFDSLG NKNALFGIIQ GSVYEDLRDI SVKGLVDIGF DGYAVGGLAV GEPKADMHRI LEHVCPQIPA DK PRYLMGV GKPEDLVEGV RRGIDMFDCV MPTRNARNGH LFVTDGVVKI RNAKYKSDTG PLDPECDCYT CRNYSRAYLH HLD RCNEIL GARLNTIHNL RYYQRLMAGL RKAIEEGKLE SFVTDFYQRQ GREVPPLNV

UniProtKB: Queuine tRNA-ribosyltransferase

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Macromolecule #2: tRNA(Tyr)

MacromoleculeName: tRNA(Tyr) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 27.178178 KDa
SequenceString:
GGUGGGGUUC CCGAGCGGCC AAAGGGAGCA GACU(HSX)UAAAU CUGCCGUCAC AGACUUCGAA GGUUCGAAUC CUUCCC CCA CCACCA

GENBANK: GENBANK: CP053281.1

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Macromolecule #3: 9-DEAZAGUANINE

MacromoleculeName: 9-DEAZAGUANINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: 9DG
Molecular weightTheoretical: 150.138 Da
Chemical component information

ChemComp-9DG:
9-DEAZAGUANINE

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 76925
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 76925
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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