[English] 日本語
Yorodumi
- PDB-3egi: Methyltransferase domain of human trimethylguanosine synthase TGS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3egi
TitleMethyltransferase domain of human trimethylguanosine synthase TGS1 bound to m7GpppA (inactive form)
ComponentsTrimethylguanosine synthase homolog
KeywordsTRANSFERASE / methyltransferase-domain / alpha-beta-alpha sandwich / Methyltransferase / Nucleus / Transcription / Transcription regulation
Function / homology
Function and homology information


ribonucleoprotein complex biogenesis / RNA cap trimethylguanosine synthase activity / 7-methylguanosine RNA capping / RNA methyltransferase activity / 7-methylguanosine cap hypermethylation / small nuclear ribonucleoprotein complex / spliceosomal snRNP assembly / Cajal body / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha ...ribonucleoprotein complex biogenesis / RNA cap trimethylguanosine synthase activity / 7-methylguanosine RNA capping / RNA methyltransferase activity / 7-methylguanosine cap hypermethylation / small nuclear ribonucleoprotein complex / spliceosomal snRNP assembly / Cajal body / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / Transferases; Transferring one-carbon groups; Methyltransferases / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / snRNP Assembly / nucleolus / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
RNA cap guanine-N2 methyltransferase / RNA cap guanine-N2 methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Trimethylguanosine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsMonecke, T. / Dickmanns, A. / Ficner, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure analysis of the conserved methyltransferase domain of human trimethylguanosine synthase TGS1.
Authors: Monecke, T. / Dickmanns, A. / Strasser, A. / Ficner, R.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trimethylguanosine synthase homolog
B: Trimethylguanosine synthase homolog
C: Trimethylguanosine synthase homolog
D: Trimethylguanosine synthase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8918
Polymers91,1824
Non-polymers1,7094
Water11,367631
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.893, 213.893, 62.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

21C-424-

HOH

-
Components

#1: Protein
Trimethylguanosine synthase homolog / Nuclear receptor coactivator 6-interacting protein / PRIP-interacting protein with ...Nuclear receptor coactivator 6-interacting protein / PRIP-interacting protein with methyltransferase motif / PIPMT / PIMT / CLL-associated antigen KW-2 / Hepatocellular carcinoma-associated antigen 137


Mass: 22795.551 Da / Num. of mol.: 4 / Fragment: RNA-methyltransferase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGS1, HCA137, NCOA6IP, PIMT / Plasmid: pGex-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q96RS0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: Na-Formate, pH 6.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9799, 0.9801
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 5, 2006
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97991
20.98011
ReflectionResolution: 2.2→50 Å / Num. all: 73095 / Num. obs: 71001 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 8.7 % / Rmerge(I) obs: 0.048
Reflection shellResolution: 2.2→2.28 Å / Num. unique all: 15867

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.21→39.9 Å / σ(F): 3.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.252 3224 RANDOM
Rwork0.21 --
all-71603 -
obs-69455 -
Refinement stepCycle: LAST / Resolution: 2.21→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 108 631 6733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.291
X-RAY DIFFRACTIONr_bond_refined_d0.01

+
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://pdbjlvh1.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