[English] 日本語
- PDB-6qe0: Structure of E.coli RlmJ in complex with a bisubstrate analogue (BA2) -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6qe0
TitleStructure of E.coli RlmJ in complex with a bisubstrate analogue (BA2)
ComponentsRibosomal RNA large subunit methyltransferase J
KeywordsTRANSFERASE / RNA MTases / methyltransferase / m6A / transition state analogue / inhibitor / RNA binding / TrmK / RlmJ / m1A / structure.
Function / homology
Function and homology information

23S rRNA (adenine(2030)-N(6))-methyltransferase activity / 23S rRNA (adenine2030-N6)-methyltransferase / rRNA (adenine-N6-)-methyltransferase activity / carbon utilization / rRNA base methylation / RNA binding / cytosol
Similarity search - Function
Ribosomal RNA large subunit methyltransferase J / Ribosomal RNA large subunit methyltransferase D, RlmJ / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HZ2 / Ribosomal RNA large subunit methyltransferase J / Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
AuthorsOerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C.
CitationJournal: Rna Biol. / Year: 2019
Title: Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites.
Authors: Oerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C.
DepositionJan 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: Ribosomal RNA large subunit methyltransferase J
hetero molecules

Theoretical massNumber of molelcules
Total (without water)32,9332

  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12400 Å2
Unit cell
Length a, b, c (Å)47.820, 58.400, 49.230
Angle α, β, γ (deg.)90.00, 97.32, 90.00
Int Tables number4
Space group name H-MP1211


#1: Protein Ribosomal RNA large subunit methyltransferase J / / 23STSA4 / rRNA (adenine(2030)-N6)-methyltransferase / 23S rRNA m6A2030 methyltransferase

Mass: 32271.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yhiR, rlmJ, PPECC33_03818 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0G3KF30, UniProt: P37634*PLUS, 23S rRNA (adenine2030-N6)-methyltransferase
#2: Chemical ChemComp-HZ2 / (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[2-[[9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]ethyl]amino]-2-azanyl-butanoic acid

Mass: 660.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36N12O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-Tris pH 6.5, 25% (w/v) PEG3350

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.39→37.46 Å / Num. obs: 53277 / % possible obs: 98.68 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.0759 / Net I/σ(I): 12.71
Reflection shellResolution: 1.39→1.44 Å / Rmerge(I) obs: 2.033


PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLV
Resolution: 1.394→37.46 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.12
RfactorNum. reflection% reflection
Rfree0.2664 2642 4.99 %
Rwork0.2244 --
obs0.2265 52895 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.394→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 47 264 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062344
X-RAY DIFFRACTIONf_angle_d0.93181
X-RAY DIFFRACTIONf_dihedral_angle_d16.552889
X-RAY DIFFRACTIONf_chiral_restr0.075345
X-RAY DIFFRACTIONf_plane_restr0.005402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3944-1.41970.46021170.44642292X-RAY DIFFRACTION87
1.4197-1.4470.50671400.4522668X-RAY DIFFRACTION99
1.447-1.47660.45781370.43972592X-RAY DIFFRACTION99
1.4766-1.50870.45221400.4382658X-RAY DIFFRACTION99
1.5087-1.54380.47331400.42792661X-RAY DIFFRACTION99
1.5438-1.58240.44611410.39332634X-RAY DIFFRACTION98
1.5824-1.62520.43461380.38652609X-RAY DIFFRACTION99
1.6252-1.6730.42361360.37392625X-RAY DIFFRACTION99
1.673-1.7270.38311380.35512663X-RAY DIFFRACTION99
1.727-1.78870.44071410.35882657X-RAY DIFFRACTION100
1.7887-1.86040.33571400.32282654X-RAY DIFFRACTION100
1.8604-1.9450.32061410.27032685X-RAY DIFFRACTION100
1.945-2.04760.30621400.24942669X-RAY DIFFRACTION100
2.0476-2.17590.3031420.24572690X-RAY DIFFRACTION100
2.1759-2.34390.29671410.2432687X-RAY DIFFRACTION100
2.3439-2.57970.24971400.21592657X-RAY DIFFRACTION100
2.5797-2.9530.2451420.19452691X-RAY DIFFRACTION100
2.953-3.72020.22621430.16572713X-RAY DIFFRACTION100
3.7202-47.45770.16751450.15172748X-RAY DIFFRACTION100

About Yorodumi


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


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