[English] 日本語
Yorodumi
- PDB-1d9n: SOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE METHYL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d9n
TitleSOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE METHYLATION-DEPENDENT TRANSCRIPTIONAL REPRESSOR MBD1/PCM1
ComponentsMETHYL-CPG-BINDING PROTEIN MBD1
KeywordsGENE REGULATION / MBD / METHYL-CPG / PCM1 / METHYLATION / DNA BINDING DOMAIN
Function / homology
Function and homology information


double-stranded methylated DNA binding / unmethylated CpG binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / SUMOylation of transcription cofactors / nuclear matrix / chromosome / transcription by RNA polymerase II / nuclear speck / negative regulation of DNA-templated transcription ...double-stranded methylated DNA binding / unmethylated CpG binding / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / SUMOylation of transcription cofactors / nuclear matrix / chromosome / transcription by RNA polymerase II / nuclear speck / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / negative regulation of transcription by RNA polymerase II / 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
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 3.8.
AuthorsOhki, I. / Shimotake, N. / Fujita, N. / Nakao, M. / Shirakawa, M.
Citation
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.
#1: 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.
#2: Journal: Mol.Cell.Biol. / Year: 1999
Title: Methylation-mediated Transcriptional Silencing in Euchromatin by Methyl-CpG Binding Protein MBD1 Isoforms
Authors: Fujita, N. / Takebayashi, S. / Okumura, K. / Kudo, S. / Chiba, T. / Saya, H. / Nakao, M.
History
DepositionOct 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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
A: METHYL-CPG-BINDING PROTEIN MBD1


Theoretical massNumber of molelcules
Total (without water)8,5171
Polymers8,5171
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)25 / 125structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein METHYL-CPG-BINDING PROTEIN MBD1


Mass: 8516.751 Da / Num. of mol.: 1 / Fragment: METHYL-CPG-BINDING DOMAIN OF MBD1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
1314D 13C/13C-SEPARATED NOESY
1414D 13C/15N-SEPARATED NOESY
151HMQC-J
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTI-DIMENSIONAL HETERONUCLEAR NMR SPECTROSCOPY.

-
Sample preparation

DetailsContents: 1.3MM MBD U-15N,13C; 20MM PHOSPHATE BUFFER; 50MM KCL; 5MM DTT
Sample conditionsIonic strength: 50mM KCL / pH: 6.5 / Pressure: 1 ATMOSPHERE / 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
NMRPipe1.7DELAGLIOprocessing
PIPP97NOVGARRETTdata analysis
X-PLOR3.8BRUNGERrefinement
RefinementMethod: STRUCTURE CALCULATIONS WERE PERFORMED FOLLOWING SIMULATED ANNEALING PROTOCOLS USING X-PLOR 3.8.
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1270 NOE CONSTRAINTS, 44 DIHEDRAL ANGLE CONSTRAINTS AND 15 HYDROGEN BONDS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 125 / Conformers submitted total number: 25

+
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