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- PDB-2d2w: Solution structure and Dynamics of the DNA-Binding Domain of Myoc... -

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Basic information

Entry
Database: PDB / ID: 2d2w
TitleSolution structure and Dynamics of the DNA-Binding Domain of Myocyte Nuclear Factor
ComponentsForkhead box protein K1
KeywordsDNA BINDING PROTEIN / DNA-binding domain / winged-helix / Forkhead
Function / homology
Function and homology information


UCH proteinases / canonical glycolysis / muscle organ development / intracellular glucose homeostasis / response to starvation / 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 / intracellular glucose homeostasis / response to starvation / 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 / distance geometry, simulated annealing
AuthorsChuang, W.-J. / Chang, C.-H. / Jeng, W.-Y. / Chu, Y.-P.
CitationJournal: TO BE PUBLISHED
Title: Solution Structure and Backbone Dynamics of the DNA-Binding Domain of Myocyte Nuclear Factor (Foxk1)
Authors: Chang, C.-H. / Chu, Y.-P. / Jeng, W.-Y. / Chuang, W.-J.
History
DepositionSep 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Forkhead box protein K1


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

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Components

#1: Protein Forkhead box protein K1 / Myocyte nuclear factor / 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 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42128

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Experimental details

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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(CACBCO)NH, HCCH-TOCSY, HCCH-COSY

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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

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1refinement
AURELIA2.7.10Neidigdata analysis
XwinNMR2.6Brukerprocessing
RefinementMethod: distance geometry, simulated annealing / 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

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