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- PDB-2rms: Solution structure of the mSin3A PAH1-SAP25 SID complex -

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Basic information

Entry
Database: PDB / ID: 2rms
TitleSolution structure of the mSin3A PAH1-SAP25 SID complex
Components
  • MSin3A-binding protein
  • Paired 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 / activation of innate immune response / positive regulation of neuron differentiation / 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 / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA replication / negative regulation of DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / nucleolus / regulation of DNA-templated transcription / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Helix Hairpins - #710 / Histone deacetylase complex subunit SAP25 / Histone deacetylase complex subunit SAP25 / 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 ...Helix Hairpins - #710 / Histone deacetylase complex subunit SAP25 / Histone deacetylase complex subunit SAP25 / 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. / Helix Hairpins / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone deacetylase complex subunit SAP25 / 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paired amphipathic helix protein Sin3a
B: MSin3A-binding protein


Theoretical massNumber of molelcules
Total (without water)14,2282
Polymers14,2282
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
#2: Protein MSin3A-binding protein / SAP25 SID domain / Transcriptional corepressor SAP25 / Histone deacetylase associated SIN3 ...SAP25 SID domain / Transcriptional corepressor SAP25 / Histone deacetylase associated SIN3 corepressor complex subunit SAP25


Mass: 6145.596 Da / Num. of mol.: 1 / Fragment: UNP residues 126-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sap25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1EHW4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-15N NOESY
1333D 1H-13C NOESY
1443D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1.0mM [U-15N] SIN3A, 0.7-1.0mM SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.7-1.0mM SIN3A, 0.7-1.0mM [U-15N] SAP25, 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, 0.7-1.0mM SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 100% D2O100% D2O
40.7-1.0mM SIN3A , 0.7-1.0mM [U-13C; U-15N] SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMSIN3A[U-15N]1
0.7 mMSAP251
20 mMsodium phosphate1
2 mMDTT1
0.2 %sodium azide1
0.7 mMSIN3A2
0.7 mMSAP25[U-15N]2
20 mMsodium phosphate2
2 mMDTT2
0.2 %sodium azide2
0.7 mMSIN3A[U-13C; U-15N]3
0.7 mMSAP253
20 mMsodium phosphate3
2 mMDTT3
0.2 %sodium azide3
0.7 mMSIN3A4
0.7 mMSAP25[U-13C; U-15N]4
20 mMsodium phosphate4
2 mMDTT4
0.2 %sodium azide4
Sample conditionsIonic strength: .02 / pH: 6 / Pressure: ambient / Temperature: 303 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
VNMRVariancollection
ARIA1.2Linge, O'Donoghue, Nilgesdata analysis
Felix98Accelrys Software Inc.processing
Felix98Accelrys Software Inc.peak picking
Felix98Accelrys Software Inc.data analysis
CNSBrunger, Adams, Clore, Gros, Nilges, Readstructure solution
CNSBrunger, 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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