[English] 日本語
Yorodumi
- PDB-6ajk: Crystal structure of TFB1M and h45 in homo sapiens -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ajk
TitleCrystal structure of TFB1M and h45 in homo sapiens
Components
  • Dimethyladenosine transferase 1, mitochondrial
  • RNA (28-MER)
KeywordsTRANSFERASE/RNA / TFB1M / helix45 / TRANSFERASE-RNA complex
Function / homology
Function and homology information


rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / S-adenosyl-L-methionine binding / rRNA methylation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis ...rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / S-adenosyl-L-methionine binding / rRNA methylation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis / mitochondrial matrix / mitochondrion / DNA binding / RNA binding
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Dimethyladenosine transferase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsLiu, X. / Shen, S. / Wu, P. / Li, F. / Wang, C. / Gong, Q. / Wu, J. / Zhang, H. / Shi, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (China)31330018,31870760 China
Chinese Academy of SciencesXDPB10 China
Chinese Academy of SciencesXDB08010101 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function.
Authors: Liu, X. / Shen, S. / Wu, P. / Li, F. / Liu, X. / Wang, C. / Gong, Q. / Wu, J. / Yao, X. / Zhang, H. / Shi, Y.
History
DepositionAug 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dimethyladenosine transferase 1, mitochondrial
B: RNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)45,7892
Polymers45,7892
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-9 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.564, 122.564, 73.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

-
Components

#1: Protein Dimethyladenosine transferase 1, mitochondrial / Mitochondrial 12S rRNA dimethylase 1 / Mitochondrial transcription factor B1 / mtTFB1 / S- ...Mitochondrial 12S rRNA dimethylase 1 / Mitochondrial transcription factor B1 / mtTFB1 / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase 1


Mass: 36753.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFB1M, CGI-75 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WVM0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain RNA (28-MER)


Mass: 9035.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M sodium citrate, pH 5.0, 20% PEG 8000

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 11458 / % possible obs: 98.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 30.25 Å2 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.101 / Rrim(I) all: 0.273 / Χ2: 0.46 / Net I/σ(I): 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.116.50.81911360.7810.3220.8860.43399.6
3.11-3.236.50.58211360.8570.2280.6290.42399.2
3.23-3.386.40.46311160.8810.1820.5010.45199.2
3.38-3.566.30.38411270.8730.1530.4160.47699
3.56-3.786.20.29711380.90.1190.3220.46699
3.78-4.075.50.21511500.9710.0940.2360.46499.5
4.07-4.4860.16311340.980.0670.1770.46998.6
4.48-5.136.50.14811410.9810.0570.160.4797
5.13-6.466.20.17911460.980.0710.1940.45996.2
6.46-405.60.09912340.9940.0410.1080.49996.3

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GC5

4gc5


Resolution: 3.001→37.271 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 20.58
RfactorNum. reflection% reflection
Rfree0.2411 551 4.82 %
Rwork0.1965 --
obs0.1988 11431 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.61 Å2 / Biso mean: 24.7873 Å2 / Biso min: 10.31 Å2
Refinement stepCycle: final / Resolution: 3.001→37.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 601 0 0 2944
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073068
X-RAY DIFFRACTIONf_angle_d0.9524293
X-RAY DIFFRACTIONf_chiral_restr0.049504
X-RAY DIFFRACTIONf_plane_restr0.007451
X-RAY DIFFRACTIONf_dihedral_angle_d11.0641799
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0008-3.30260.28521160.23872714283099
3.3026-3.78010.25041330.21092688282199
3.7801-4.76090.23851550.16992693284899
4.7609-37.27420.21411470.18542785293296

+
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