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- PDB-9j5p: Crystal structure of B. subtilis CspR complexed with sinefungin a... -

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Basic information

Entry
Database: PDB / ID: 9j5p
TitleCrystal structure of B. subtilis CspR complexed with sinefungin and cellularly expressed tRNA Leu
Components
  • Putative tRNA (cytidine(34)-2'-O)-methyltransferase
  • tRNA Leu (89-MER)
KeywordsTRANSFERASE / Methyltransferase / tRNA post-transcriptional modification / CspR 2'-O-methylribosylation / TRANSFERASE-RNA complex
Function / homology
Function and homology information


wobble position ribose methylation / tRNA (cytidine(34)-2'-O)-methyltransferase activity / tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity / tRNA (cytidine34-2'-O)-methyltransferase / RNA binding / cytoplasm
Similarity search - Function
tRNA (cytidine/uridine-2'-O-)-methyltransferase / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
SINEFUNGIN / RNA / RNA (> 10) / Putative tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsYoo, J. / Kim, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural and functional characterization of CspR, a 2'-O-methyltransferase acting on wobble position within tRNA.
Authors: Yoo, J. / Lee, Y. / Cho, G. / Lim, J. / Kim, J.
History
DepositionAug 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 27, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA Leu (89-MER)
B: Putative tRNA (cytidine(34)-2'-O)-methyltransferase
C: Putative tRNA (cytidine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7644
Polymers68,3833
Non-polymers3811
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-12 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.833, 136.833, 184.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: RNA chain tRNA Leu (89-MER)


Mass: 28950.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Escherichia coli K-12 (bacteria)
#2: Protein Putative tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine/uridine-2'-O-)-methyltransferase CspR


Mass: 19716.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: cspR, ygaR, BSU08930 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O31590, tRNA (cytidine34-2'-O)-methyltransferase
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 70.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5) 1.4 M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 3.18→44.78 Å / Num. obs: 14622 / % possible obs: 94 % / Redundancy: 38.7 % / CC1/2: 0.994 / Net I/σ(I): 10.5
Reflection shellResolution: 3.182→3.353 Å / Num. unique obs: 871 / CC1/2: 0.362

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
MxDCdata collection
xia2data reduction
STARANISOdata scaling
PHASERphasing
Coot0.9.2model building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-O31590_F1,5ON2

5on2


Resolution: 3.18→36.18 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 767 5.25 %
Rwork0.2159 --
obs0.2178 14605 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.18→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 1918 27 0 4512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034801
X-RAY DIFFRACTIONf_angle_d0.576943
X-RAY DIFFRACTIONf_dihedral_angle_d12.8151448
X-RAY DIFFRACTIONf_chiral_restr0.035839
X-RAY DIFFRACTIONf_plane_restr0.005556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.430.3339730.33061398X-RAY DIFFRACTION43
3.43-3.770.36331370.27262427X-RAY DIFFRACTION74
3.77-4.320.25891590.23453140X-RAY DIFFRACTION95
4.32-5.440.25042140.20683314X-RAY DIFFRACTION100
5.44-36.180.22031840.19343559X-RAY DIFFRACTION100

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