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- PDB-2f05: Solution structure of free PAH2 domain of mSin3B -

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Basic information

Entry
Database: PDB / ID: 2f05
TitleSolution structure of free PAH2 domain of mSin3B
ComponentsPaired amphipathic helix protein Sin3b
KeywordsTRANSCRIPTION REPRESSOR / 4 helix bundle
Function / homology
Function and homology information


autosome / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / XY body / cardiac muscle tissue development / Sin3-type complex / Y chromosome / X chromosome / negative regulation of cell cycle ...autosome / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / XY body / cardiac muscle tissue development / Sin3-type complex / Y chromosome / X chromosome / negative regulation of cell cycle / skeletal muscle tissue development / negative regulation of cell migration / transcription corepressor activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Paired amphipathic helix / Paired amphipathic helix 2 (pah2 repeat) / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily ...Paired amphipathic helix / Paired amphipathic helix 2 (pah2 repeat) / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily / Paired amphipathic helix repeat / PAH domain profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Paired amphipathic helix protein Sin3b
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, with water-refinement
Authorsvan Ingen, H. / Baltussen, M.A. / Aelen, J. / Vuister, G.W.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Role of Structural and Dynamical Plasticity in Sin3: The Free PAH2 Domain is a Folded Module in mSin3B
Authors: van Ingen, H. / Baltussen, M.A. / Aelen, J. / Vuister, G.W.
History
DepositionNov 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Paired amphipathic helix protein Sin3b


Theoretical massNumber of molelcules
Total (without water)12,2421
Polymers12,2421
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Paired amphipathic helix protein Sin3b / Transcriptional corepressor Sin3b / Histone deacetylase complex subunit Sin3b


Mass: 12241.564 Da / Num. of mol.: 1 / Fragment: PAH2 domain (residues 148-252)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sin3b, Kiaa0700 / Plasmid: pGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q62141

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 0.9 mM PAH2 uniform 13C/15N labeled, H2O, 100mM KCl, 50 mM Pi buffer pH 6.3
Solvent system: H2O, 100mM KCl, 50 mM Pi buffer pH 6.3
Sample conditionsIonic strength: 150 / pH: 6.3 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.05GUENTERTrefinement
X-PLORBRUNGERrefinement
RefinementMethod: simulated annealing, with water-refinement / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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