[English] 日本語
Yorodumi
- PDB-1ig4: Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ig4
TitleSolution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA
Components
  • 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'
  • Methyl-CpG Binding Protein
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / ALPHA-BETA / DOUBLE HELIX / RECOGNITION VIA BETA-SHEET / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / methyl-CpG binding / negative regulation of astrocyte differentiation / epigenetic regulation of gene expression / response to nutrient levels / SUMOylation of transcription cofactors / response to cocaine / neuron differentiation ...double-stranded methylated DNA binding / ventricular cardiac muscle tissue development / unmethylated CpG binding / methyl-CpG binding / negative regulation of astrocyte differentiation / epigenetic regulation of gene expression / response to nutrient levels / SUMOylation of transcription cofactors / response to cocaine / neuron differentiation / nuclear matrix / response to estradiol / transcription by RNA polymerase II / nuclear speck / response to xenobiotic stimulus / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily ...Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Methyl-CpG-binding domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Structure calculations were performed following simulated annealing protocols using X-PLOR.
AuthorsOhki, I. / Shimotake, N. / Fujita, N. / Jee, J.-G. / Ikegami, T. / Nakao, M. / Shirakawa, M.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.
Authors: Ohki, I. / Shimotake, N. / Fujita, N. / Jee, J. / Ikegami, T. / Nakao, M. / Shirakawa, M.
#1: Journal: Embo J. / Year: 1999
Title: Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1
Authors: Ohki, I. / Shimotake, N. / Fujita, N. / Nakao, M. / Shirakawa, M.
#2: Journal: Nat.Genet. / Year: 1997
Title: A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins
Authors: Cross, S.H. / Meehan, R.R. / Nan, X. / Bird, A.
History
DepositionApr 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'
C: 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'
A: Methyl-CpG Binding Protein


Theoretical massNumber of molelcules
Total (without water)15,8703
Polymers15,8703
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: DNA chain 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'


Mass: 3676.431 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Methyl-CpG Binding Protein


Mass: 8516.751 Da / Num. of mol.: 1 / Fragment: Methyl-CpG-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MBD1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q9UIS9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-separated NOESY
1224D 13C-separated NOESY
1333D 15N-separated NOESY
1423D 13C-filtered 13C-separated NOESY
153HNHA
NMR detailsText: The structure was determined using multi-dimensional heteronuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.3mM MBD1(U-15N,13C)-DNA Complex; 20mM phosphate buffer90% H2O/10% D2O
21.3mM MBD1(U-15N,13C)-DNA Complex; 20mM phosphate buffer100% D2O
31mM MBD1(U-15N)-DNA Complex; 20mM phosphate buffer90% H2O/10% D2O
Sample conditionspH: 6.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX5002
Bruker DRXBrukerDRX8003

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delaglioprocessing
PIPP4.0.4Garrettdata analysis
NMRView4Johnsondata analysis
X-PLOR3.8Brungerrefinement
RefinementMethod: Structure calculations were performed following simulated annealing protocols using X-PLOR.
Software ordinal: 1
Details: The structure was determined from a total of 2,022 distance and dihedral angle restraints, including 91 intermolecular NOE restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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