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- PDB-2rmr: Solution structure of mSin3A PAH1 domain -

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Basic information

Entry
Database: PDB / ID: 2rmr
TitleSolution structure of mSin3A PAH1 domain
ComponentsPaired amphipathic helix protein Sin3a
KeywordsTRANSCRIPTION / Protein/Protein interaction / PAH domain / SIN3 corepressor / Transcription repression / Transcription regulation
Function / homology
Function and homology information


Regulation of MECP2 expression and activity / response to methylglyoxal / SUMOylation of transcription cofactors / regulation of hormone levels / cerebral cortex neuron differentiation / negative regulation of circadian rhythm / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / negative regulation of stem cell population maintenance ...Regulation of MECP2 expression and activity / response to methylglyoxal / SUMOylation of transcription cofactors / regulation of hormone levels / cerebral cortex neuron differentiation / negative regulation of circadian rhythm / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / negative regulation of stem cell population maintenance / cellular response to dopamine / transcription regulator inhibitor activity / negative regulation of protein localization to nucleus / regulation of axon extension / positive regulation of stem cell population maintenance / Sin3-type complex / type I interferon-mediated signaling pathway / histone deacetylase complex / hematopoietic progenitor cell differentiation / heterochromatin formation / positive regulation of defense response to virus by host / response to organonitrogen compound / positive regulation of G2/M transition of mitotic cell cycle / transcription repressor complex / positive regulation of neuron differentiation / activation of innate immune response / negative regulation of cell migration / cellular response to glucose stimulus / negative regulation of transforming growth factor beta receptor signaling pathway / protein localization / kinetochore / transcription corepressor activity / rhythmic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / DNA replication / transcription regulator complex / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / regulation of DNA-templated transcription / nucleolus / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus
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 Sin3a
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsSahu, S.C. / Swanson, K.A. / Kang, R.S. / Huang, K. / Brubaker, K. / Ratcliff, K. / Radhakrishnan, I.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Conserved Themes in Target Recognition by the PAH1 and PAH2 Domains of the Sin3 Transcriptional Corepressor
Authors: Sahu, S.C. / Swanson, K.A. / Kang, R.S. / Huang, K. / Brubaker, K. / Ratcliff, K. / Radhakrishnan, I.
History
DepositionNov 14, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Paired amphipathic helix protein Sin3a


Theoretical massNumber of molelcules
Total (without water)8,0821
Polymers8,0821
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)20 / 80structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Paired amphipathic helix protein Sin3a / SIN3A PAH1 Domain / Transcriptional corepressor / SIN3A / Histone deacetylase associated sin3 ...SIN3A PAH1 Domain / Transcriptional corepressor / SIN3A / Histone deacetylase associated sin3 corepressor complex subunit SIN3A


Mass: 8082.224 Da / Num. of mol.: 1 / Fragment: UNP residues 119-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sin3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q60520

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1.0mM [U-13C; U-15N] Sin3A PAH1 domain, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 100% D2O100% D2O
20.7-1.0mM [U-15N] Sin3A PAH1 domain, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.7-1.0mM [U-13C; U-15N] Sin3A PAH1 domain, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMSin3A PAH1 domain[U-13C; U-15N]1
20 mMsodium phosphate1
2 mMDTT1
0.2 %sodium azide1
0.7 mMSin3A PAH1 domain[U-15N]2
20 mMsodium phosphate2
2 mMDTT2
0.2 %sodium azide2
0.7 mMSin3A PAH1 domain[U-13C; U-15N]3
20 mMsodium phosphate3
2 mMDTT3
0.2 %sodium azide3
Sample conditionsIonic strength: .02 / pH: 6 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges, Readstructure solution
Felix98Accelrys Software Inc.processing
Felix98Accelrys Software Inc.peak picking
Felix98Accelrys Software Inc.data analysis
ARIA1.2Linge, O'Donoghue, Nilgesdata analysis
VNMRVariancollection
CNS1.2Brunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

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