[English] 日本語
Yorodumi
- PDB-8w9u: Crystal structure of CspR from Bacillus subtilis complexed with SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8w9u
TitleCrystal structure of CspR from Bacillus subtilis complexed with SAH
ComponentsPutative tRNA (cytidine(34)-2'-O)-methyltransferase
KeywordsTRANSFERASE / Methyltransferase / tRNA post-transcriptional modification / CspR / tRNA 2'-O-methyltransferase
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
S-ADENOSYL-L-HOMOCYSTEINE / 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: 1.85 Å
AuthorsLee, Y. / 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
DepositionSep 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_entry_details
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _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 / _pdbx_entry_details.has_protein_modification
Revision 1.2Aug 27, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,7869
Polymers43,5412
Non-polymers1,2457
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-90 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.763, 46.959, 50.090
Angle α, β, γ (deg.)110.33, 92.71, 106.56
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Putative tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine/uridine-2'-O-)-methyltransferase CspR


Mass: 21770.533 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Potassium sodium tartrate tetrahydrate, Sodium citrate tribasic dihydrate pH 5.6, ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.85→39.2 Å / Num. obs: 24862 / % possible obs: 90.52 % / Redundancy: 3.8 % / Biso Wilson estimate: 26.19 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.1298 / Net I/σ(I): 4.56
Reflection shellResolution: 1.85→1.916 Å / Num. unique obs: 1626 / CC1/2: 0.752

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158:000)refinement
Cootmodel building
XDSdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.85→39.2 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1279 5.15 %
Rwork0.1947 --
obs0.197 24848 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 78 89 2503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072468
X-RAY DIFFRACTIONf_angle_d1.0483368
X-RAY DIFFRACTIONf_dihedral_angle_d17.813351
X-RAY DIFFRACTIONf_chiral_restr0.063386
X-RAY DIFFRACTIONf_plane_restr0.007425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.3035900.29961728X-RAY DIFFRACTION60
1.92-2.010.30621340.24822409X-RAY DIFFRACTION83
2.01-2.120.29441470.2192758X-RAY DIFFRACTION96
2.12-2.250.22931560.19762806X-RAY DIFFRACTION96
2.25-2.420.25541410.19792797X-RAY DIFFRACTION97
2.42-2.670.2941420.19952807X-RAY DIFFRACTION97
2.67-3.050.22361430.19462807X-RAY DIFFRACTION97
3.05-3.850.23581720.1762752X-RAY DIFFRACTION96
3.85-39.20.20611540.1852705X-RAY DIFFRACTION94

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more