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- EMDB-75124: E. coli tRNA guanine transgylcosylase -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75124
TitleE. coli tRNA guanine transgylcosylase
Map data
Sample
  • Complex: E. coli TGT
    • Protein or peptide: Queuine tRNA-ribosyltransferase
  • Ligand: ZINC ION
KeywordsTGT / RNA modifying enzyme / TRANSFERASE
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: 3.52 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: 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 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75124.png

Downloads & links

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Map

FileDownload / File: emd_75124.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.252
Minimum - Maximum-1.0972993 - 1.5760846
Average (Standard dev.)0.00091923954 (±0.040681098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75124_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_75124_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 : E. coli TGT

EntireName: E. coli TGT
Components
  • Complex: E. coli TGT
    • Protein or peptide: Queuine tRNA-ribosyltransferase
  • Ligand: ZINC ION

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Supramolecule #1: E. coli TGT

SupramoleculeName: E. coli TGT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: N-terminal STREP tag C-terminal His tag / Number of copies: 4 / Enantiomer: LEVO / EC number: tRNA-guanosine34 preQ1 transglycosylase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 44.579715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWSHPQFEKG KFELDTTDGR ARRGRLVFDR GVVETPCFMP VGTYGTVKGM TPEEVEATGA QIILGNTFHL WLRPGQEIMK LHGDLHDFM QWKGPILTDS GGFQVFSLGD IRKITEQGVH FRNPINGDPI FLDPEKSMEI QYDLGSDIVM IFDECTPYPA D WDYAKRSM ...String:
MWSHPQFEKG KFELDTTDGR ARRGRLVFDR GVVETPCFMP VGTYGTVKGM TPEEVEATGA QIILGNTFHL WLRPGQEIMK LHGDLHDFM QWKGPILTDS GGFQVFSLGD IRKITEQGVH FRNPINGDPI FLDPEKSMEI QYDLGSDIVM IFDECTPYPA D WDYAKRSM EMSLRWAKRS RERFDSLGNK NALFGIIQGS VYEDLRDISV KGLVDIGFDG YAVGGLAVGE PKADMHRILE HV CPQIPAD KPRYLMGVGK PEDLVEGVRR GIDMFDCVMP TRNARNGHLF VTDGVVKIRN AKYKSDTGPL DPECDCYTCR NYS RAYLHH LDRCNEILGA RLNTIHNLRY YQRLMAGLRK AIEEGKLESF VTDFYQRQGR EVPPLNVDHH HHHH

UniProtKB: Queuine tRNA-ribosyltransferase

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / 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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio model
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 89837
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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