[English] 日本語
Yorodumi
- PDB-2a3s: Solution structure and Dynamics of DNA-Binding Domain of Myocyte ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a3s
TitleSolution structure and Dynamics of DNA-Binding Domain of Myocyte Nuclear Factor
ComponentsMyocyte Nuclear Factor
KeywordsDNA BINDING PROTEIN / DNA-BINDING DOMAIN / WINGED-HELIX / Forkhead
Function / homology
Function and homology information


UCH proteinases / canonical glycolysis / muscle organ development / response to starvation / intracellular glucose homeostasis / negative regulation of cell cycle / regulation of glucose metabolic process / 14-3-3 protein binding / negative regulation of autophagy / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...UCH proteinases / canonical glycolysis / muscle organ development / response to starvation / intracellular glucose homeostasis / negative regulation of cell cycle / regulation of glucose metabolic process / 14-3-3 protein binding / negative regulation of autophagy / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of cell growth / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleus / cytoplasm
Similarity search - Function
: / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Forkhead associated domain ...: / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Forkhead box protein K1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Hybrid distance geometry-simulated annealing method
AuthorsChuang, W.-J. / Chang, C.-H. / Jeng, W.-Y. / Chu, Y.-P.
CitationJournal: to be published
Title: Solution structure and Dynamics of DNA-Binding Domain of Myocyte Nuclear Factor
Authors: Chuang, W.-J. / Chang, C.-H. / Jeng, W.-Y. / Chu, Y.-P.
History
DepositionJun 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myocyte Nuclear Factor


Theoretical massNumber of molelcules
Total (without water)11,7881
Polymers11,7881
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Myocyte Nuclear Factor / Forkhead box protein K1 / MNF


Mass: 11788.293 Da / Num. of mol.: 1 / Fragment: DNA-Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Foxk1(AMINO ACID 287-387) / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42128

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1333D 15N-separated NOESY
1443D 13C-separated NOESY
NMR detailsText: HNCA, HN(CO)CA, HNCACB, CBCA(CO)NH, HBHA(CACB)NH, HBHA(CBCACO)NH, HCCH-TOCSY, HCCH-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
13mM MNF; 25mM phosphate buffer; 100mM NaCl90% H2O/10% D2O
23mM MNF; 25mM phosphate buffer; 100mM NaCl100% D2O
33mM MNF U-15N; 25mM phosphate buffer; 100mM NaCl90% H2O/10% D2O
43mM MNF U-15N, 13C; 25mM phosphate buffer; 100mM NaCl90% H2O/10% D2O
Sample conditionsIonic strength: 125 / pH: 6 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerrefinement
AURELIA2.7.10Neidigdata analysis
XwinNMR2.6Brukerprocessing
RefinementMethod: Hybrid distance geometry-simulated annealing method / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / 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