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- EMDB-61148: Cryo-EM structure of TrhO from B. subtilis complexed with tRNA Ala -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61148
TitleCryo-EM structure of TrhO from B. subtilis complexed with tRNA Ala
Map dataDeepEMhancer sharpened map
Sample
  • Complex: Bacillus subtilis TrhO complexed with Alanine-specific tRNA
    • Protein or peptide: tRNA uridine(34) hydroxylase
    • RNA: RNA (76-MER)
  • Ligand: ZINC ION
KeywordsHydroxylase / tRNA post-transcriptional modification / TrhO / ho5U / Hydroxylase-RNA complex / RNA BINDING PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / tRNA modification / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
Similarity search - Function
Rhodanase, C-terminal / Rhodanase C-terminal / tRNA uridine(34) hydroxylase / tRNA uridine(34) hydroxylase, N-terminal / UPF0176 acylphosphatase like domain / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain
Similarity search - Domain/homology
tRNA uridine(34) hydroxylase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsShin K / Kim J
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C2009773 Korea, Republic Of
CitationJournal: Nat.Chem.Biol. / Year: 2026
Title: Unconventional monooxygenation by the O2-dependent tRNA wobble uridine hydroxylase TrhO
Authors: Shin K / Kim J
History
DepositionAug 13, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61148.png

Downloads & links

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Map

FileDownload / File: emd_61148.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 360 pix.
= 324.468 Å		0.9 Å/pix.
x 360 pix.
= 324.468 Å		0.9 Å/pix.
x 360 pix.
= 324.468 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9013 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.0017972518 - 1.6977125
Average (Standard dev.)0.0001833875 (±0.009905112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 324.46802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_61148_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_61148_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus subtilis TrhO complexed with Alanine-specific tRNA

EntireName: Bacillus subtilis TrhO complexed with Alanine-specific tRNA
Components
  • Complex: Bacillus subtilis TrhO complexed with Alanine-specific tRNA
    • Protein or peptide: tRNA uridine(34) hydroxylase
    • RNA: RNA (76-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Bacillus subtilis TrhO complexed with Alanine-specific tRNA

SupramoleculeName: Bacillus subtilis TrhO complexed with Alanine-specific tRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 65 KDa

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Macromolecule #1: tRNA uridine(34) hydroxylase

MacromoleculeName: tRNA uridine(34) hydroxylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 40.520547 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAGSHHHHHH GMASMTGGQQ MGRSGDDDDK MEKQYRVLLY YKYVPIEDPE AFREQHLAFC KELGLLGRIL VSSEGINGTV SGTVEQTEK YMETMKADPR FADMVFKIDE AEGHAFKKIF VRHKKELVTL RLEDDVDPNE TTGQHLKPAE FYEKMQDPNT I VIDARNDY ...String:
MAGSHHHHHH GMASMTGGQQ MGRSGDDDDK MEKQYRVLLY YKYVPIEDPE AFREQHLAFC KELGLLGRIL VSSEGINGTV SGTVEQTEK YMETMKADPR FADMVFKIDE AEGHAFKKIF VRHKKELVTL RLEDDVDPNE TTGQHLKPAE FYEKMQDPNT I VIDARNDY EYDLGHFRGA VRPDIEAFRE LPEWIEEHKD MLEGKKILTY CTGGVRCEKF SGWLVKQGFE DVAQLDGGIV TY GKDPEVQ GKLWDGQCYV FDERISVPVN RVEHVIVGKD YFTGEPCERY VNCANPSCNK KMICTPENEY KYMRSCSHEC RTN PRNLYV KEHNMTEEEV NARLAAIETE DHAAAE

UniProtKB: tRNA uridine(34) hydroxylase

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Macromolecule #2: RNA (76-MER)

MacromoleculeName: RNA (76-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 24.507547 KDa
SequenceString:
GGGGCCUUAG CUCAGCUGGG AGAGCGCCUG CUU(A1L3O)GCACGC AGGAGGUCAG CGGUUCGAUC CCGCUAGGCU CCAC CA

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / 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

Concentration1.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
0.2 mMC9H15O6PTCEP

Details: 25 mM HEPES (pH 7.5), 150 mM NaCl, 0.2 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 7.15 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118262
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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