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- EMDB-75126: E. coli TGT covalent intermediate with 2 tRNAs -

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Basic information

Entry
Database: EMDB / ID: EMD-75126
TitleE. coli TGT covalent intermediate with 2 tRNAs
Map data
Sample
  • Complex: tRNA-transglycosylase covalent intermediate with 2 tRNAs
    • 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: 2.72 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)GM141939 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Cryo-EM reveals that tRNA-transglycosylase can bind and act upon two tRNAs.
Authors: Alexander Harjung / Ember M Ruth / Mariusz Matyszewski / Jaehee Park / Caroline Knittel / Evan McCormack / Neal K Devaraj /
Abstract: Bacterial tRNA-guanine transglycosylases (TGT) are essential enzymes involved in tRNA modification, contributing to the virulence of multiple pathogens. TGT from was the first protein of this family ...Bacterial tRNA-guanine transglycosylases (TGT) are essential enzymes involved in tRNA modification, contributing to the virulence of multiple pathogens. TGT from was the first protein of this family to be isolated and purified, and as such has served as a model enzyme for the biochemical characterization of TGTs. TGT is also one of the most disease-relevant TGTs, sharing high sequence identity with TGTs from several human pathogenic bacteria, including spp. and spp. Notably, TGTs from some strains are sequence-identical to the enzyme. In addition, as a highly promiscuous enzyme, TGT has found use as an RNA-modification tool in chemical biology, enabling site-specific covalent RNA modification in vitro and in vivo. For these reasons, there has been significant interest in solving the structure of TGT. However, crystallization of TGT has proven difficult, and to date, structural insights have relied on surrogate TGT enzymes from other organisms. Here, we present the cryo-EM structure of TGT and its covalent intermediate with a full-length tRNA. Unexpectedly, the structure reveals that the TGT dimer binds and acts upon two tRNAs, which is unlike all other known TGTs. Closer analysis of the TGT-tRNA complex reveals several important interactions outside of the enzyme's active site, that facilitate RNA binding and stabilize the conformational change of the tRNA anticodon loop. Based on these structural insights, we were able to design improved, high-affinity, TGT substrate RNA hairpins.
History
DepositionJan 15, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75126.png

Downloads & links

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Map

FileDownload / File: emd_75126.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

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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: 4.76
Minimum - Maximum-10.951839 - 24.931166000000001
Average (Standard dev.)-0.000000000000663 (±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_75126_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_75126_half_map_1.map
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Half map: #1

Fileemd_75126_half_map_2.map
Projections & Slices
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Sample components

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Entire : tRNA-transglycosylase covalent intermediate with 2 tRNAs

EntireName: tRNA-transglycosylase covalent intermediate with 2 tRNAs
Components
  • Complex: tRNA-transglycosylase covalent intermediate with 2 tRNAs
    • 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 2 tRNAs

SupramoleculeName: tRNA-transglycosylase covalent intermediate with 2 tRNAs
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: 2
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: 2 / 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

Concentration1.00 mg/mL
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

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 83087
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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