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- PDB-1s5q: Solution Structure of Mad1 SID-mSin3A PAH2 Complex -

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Basic information

Entry
Database: PDB / ID: 1s5q
TitleSolution Structure of Mad1 SID-mSin3A PAH2 Complex
Components
  • MAD protein
  • Sin3a protein
KeywordsTRANSCRIPTION / Protein-peptide complex / Amphipathic helix motif / Four-helix bundle / Repressor-corepressor complex
Function / homology
Function and homology information


cellular response to tert-butyl hydroperoxide / Regulation of MECP2 expression and activity / Regulation of MITF-M-dependent genes involved in apoptosis / Mad-Max complex / response to methylglyoxal / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / SUMOylation of transcription cofactors / regulation of hormone levels / cerebral cortex neuron differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function ...cellular response to tert-butyl hydroperoxide / Regulation of MECP2 expression and activity / Regulation of MITF-M-dependent genes involved in apoptosis / Mad-Max complex / response to methylglyoxal / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / SUMOylation of transcription cofactors / regulation of hormone levels / cerebral cortex neuron differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of lipid metabolism by PPARalpha / negative regulation of circadian rhythm / Cytoprotection by HMOX1 / negative regulation of stem cell population maintenance / cellular response to dopamine / negative regulation of protein localization to nucleus / regulation of axon extension / type I interferon-mediated signaling pathway / Sin3-type complex / positive regulation of stem cell population maintenance / positive regulation of G2/M transition of mitotic cell cycle / hematopoietic progenitor cell differentiation / transcription regulator inhibitor activity / positive regulation of defense response to virus by host / 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 / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / intracellular protein localization / rhythmic process / heterochromatin formation / transcription regulator complex / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA replication / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Max dimerization protein 1 / 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 ...Max dimerization protein 1 / 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-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Max dimerization protein 1 / Paired amphipathic helix protein Sin3a
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Torsion angle dynamics, simulated annealing
AuthorsSwanson, K.A. / Knoepfler, P.S. / Huang, K. / Kang, R.S. / Cowley, S.M. / Laherty, C.D. / Eisenman, R.N. / Radhakrishnan, I.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: HBP1 and Mad1 repressors bind the Sin3 corepressor PAH2 domain with opposite helical orientations.
Authors: Swanson, K.A. / Knoepfler, P.S. / Huang, K. / Kang, R.S. / Cowley, S.M. / Laherty, C.D. / Eisenman, R.N. / Radhakrishnan, I.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Solution Structure of the Interacting Domains of the Mad-Sin3 Complex: Implications for Recruitment of a Chromatin-Modifying Complex
Authors: Brubaker, K. / Cowley, S.M. / Huang, K. / Loo, L. / Yochum, G.S. / Ayer, D.E. / Eisenman, R.N. / Radhakrishnan, I.
History
DepositionJan 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAD protein
B: Sin3a protein


Theoretical massNumber of molelcules
Total (without water)12,3122
Polymers12,3122
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 / 80The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
RepresentativeModel #15closest to the average

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Components

#1: Protein/peptide MAD protein / MAX dimerizer


Mass: 1968.302 Da / Num. of mol.: 1 / Fragment: Sin3 Interaction Domain (SID), Residues 6 to 21 / Source method: obtained synthetically
Details: The peptide sequence was synthesized using automated methods. The sequence is naturally found in Homo sapiens (human).
References: UniProt: Q05195
#2: Protein Sin3a protein


Mass: 10343.438 Da / Num. of mol.: 1
Fragment: Paired Amphipathic Helix 2, (PAH2 repeat), Residues 295 to 383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sin3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 15N-separated NOESY
1212D double half-filtered NOESY
1323D 13C-separated NOESY
1422D double half-filtered NOESY
1523D 13C-filtered,13C-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM 1:1 SID UNLABELED, PAH2 U-15N90% H2O/10% D2O
21.6 mM 1:1 SID UNLABELED, PAH2 U-15N,U-13C100% D2O
Sample conditionsIonic strength: 20 mM sodium phosphate, pH 6, 0.2% NaN3 / pH: 6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVarian NMR Inccollection
Felix98Accelrysprocessing
ARIA1.2Linge, Nilgesrefinement
CNS1.1Brungerrefinement
RefinementMethod: Torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
Conformers calculated total number: 80 / Conformers submitted total number: 20

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