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- PDB-9j5o: Cryo-EM structure of TrhO from B. subtilis complexed with tRNA Ala -

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Basic information

Entry
Database: PDB / ID: 9j5o
TitleCryo-EM structure of TrhO from B. subtilis complexed with tRNA Ala
Components
  • RNA (76-MER)
  • tRNA uridine(34) hydroxylase
KeywordsRNA BINDING PROTEIN / Hydroxylase / tRNA post-transcriptional modification / TrhO / ho5U / Hydroxylase-RNA complex
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
RNA / RNA (> 10) / tRNA uridine(34) hydroxylase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsShin, K. / Kim, J.
Funding support Korea, Republic Of, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA uridine(34) hydroxylase
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0943
Polymers65,0282
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein tRNA uridine(34) hydroxylase / tRNA hydroxylation protein O


Mass: 40520.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: trhO, ybfQ, BSU02330 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O31457, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: RNA chain RNA (76-MER)


Mass: 24507.547 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacillus subtilis TrhO complexed with Alanine-specific tRNA
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.065 MDa / Experimental value: NO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5 / Details: 25 mM HEPES (pH 7.5), 150 mM NaCl, 0.2 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
30.2 mMTCEPC9H15O6P1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 7.15 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118262 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034332
ELECTRON MICROSCOPYf_angle_d0.4856197
ELECTRON MICROSCOPYf_dihedral_angle_d22.5321436
ELECTRON MICROSCOPYf_chiral_restr0.035726
ELECTRON MICROSCOPYf_plane_restr0.004541

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