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- PDB-2l9s: Solution structure of Pf1 SID1-mSin3A PAH2 Complex -

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Basic information

Entry
Database: PDB / ID: 2l9s
TitleSolution structure of Pf1 SID1-mSin3A PAH2 Complex
Components
  • PHD finger protein 12
  • Paired amphipathic helix protein Sin3a
KeywordsTRANSCRIPTION / Protein-Peptide Complex / Amphipathic Helix motif
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 / phosphatidylinositol binding / negative regulation of cell migration / transcription corepressor binding / 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 / metal ion binding / nucleus
Similarity search - Function
PHD finger protein 12 / PHD finger protein 12, MRG binding domain / PHD finger protein 12, MRG binding domain superfamily / PHD finger protein 12 MRG binding domain / 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 ...PHD finger protein 12 / PHD finger protein 12, MRG binding domain / PHD finger protein 12, MRG binding domain superfamily / PHD finger protein 12 MRG binding domain / 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. / Arc Repressor Mutant, subunit A / Forkhead-associated (FHA) domain profile. / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helix non-globular / Zinc finger, PHD-type / PHD zinc finger / Special / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Paired amphipathic helix protein Sin3a / PHD finger protein 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsSenthil Kumar, G. / Xie, T. / Zhang, Y. / Radhakrishnan, I.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Solution Structure of the mSin3A PAH2-Pf1 SID1 Complex: A Mad1/Mxd1-Like Interaction Disrupted by MRG15 in the Rpd3S/Sin3S Complex.
Authors: Kumar, G.S. / Xie, T. / Zhang, Y. / Radhakrishnan, I.
History
DepositionFeb 23, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650 HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 12
B: Paired amphipathic helix protein Sin3a


Theoretical massNumber of molelcules
Total (without water)15,8102
Polymers15,8102
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/peptide PHD finger protein 12 / / PHD factor 1 / Pf1


Mass: 4993.607 Da / Num. of mol.: 1 / Fragment: sequence database residues 200-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1523, Pf1, PHF12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q96QT6
#2: Protein Paired amphipathic helix protein Sin3a / Histone deacetylase complex subunit Sin3a / Transcriptional corepressor Sin3a


Mass: 10816.877 Da / Num. of mol.: 1 / Fragment: PAH 2 domain residues 295-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kiaa4126, Sin3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q60520

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY aliphatic
1213D 1H-15N NOESY
1313D (H)CCH-COSY

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Sample preparation

DetailsContents: 0.75-1.5 mM [U-100% 13C; U-100% 15N] peptide, 0.75-1.5 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein_1-1[U-100% 13C; U-100% 15N]0.75-1.51
mMprotein_2-2[U-100% 13C; U-100% 15N]0.75-1.51
Sample conditionsIonic strength: 0 / pH: 6.00 / Pressure: ambient / Temperature: 298 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
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
ARIA1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Water refinement
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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