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- PDB-1s5r: Solution Structure of HBP1 SID-mSin3A PAH2 Complex -

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Basic information

Entry
Database: PDB / ID: 1s5r
TitleSolution Structure of HBP1 SID-mSin3A PAH2 Complex
Components
  • Sin3a protein
  • high mobility group box transcription factor 1
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 / 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 / negative regulation of circadian rhythm ...cellular response to tert-butyl hydroperoxide / Regulation of MECP2 expression and activity / Regulation of MITF-M-dependent genes involved in apoptosis / 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 / negative regulation of circadian rhythm / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / negative regulation of stem cell population maintenance / negative regulation of lipid transport / cellular response to dopamine / negative regulation of protein localization to nucleus / regulation of axon extension / type I interferon-mediated signaling pathway / transcription regulator inhibitor activity / positive regulation of stem cell population maintenance / Sin3-type complex / negative regulation of macrophage derived foam cell differentiation / hematopoietic progenitor cell differentiation / negative regulation of reactive oxygen species biosynthetic process / positive regulation of defense response to virus by host / 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 / negative regulation of transforming growth factor beta receptor signaling pathway / cellular response to glucose stimulus / kinetochore / Wnt signaling pathway / heterochromatin formation / transcription corepressor activity / rhythmic process / protein localization / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / DNA replication / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
HMG box-containing protein 1 / Ataxin, AXH domain / Ataxin, AXH domain superfamily / Ataxin-1 and HBP1 module (AXH) / AXH domain profile. / domain in Ataxins and HMG containing proteins / Paired amphipathic helix / Paired amphipathic helix 2 (pah2 repeat) / Histone deacetylase interacting domain / Sin3, C-terminal ...HMG box-containing protein 1 / Ataxin, AXH domain / Ataxin, AXH domain superfamily / Ataxin-1 and HBP1 module (AXH) / AXH domain profile. / domain in Ataxins and HMG containing proteins / 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. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Paired amphipathic helix protein Sin3a / HMG box-containing protein 1 / HMG box-containing protein 1
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.
CitationJournal: 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.
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: high mobility group box transcription factor 1
B: Sin3a protein


Theoretical massNumber of molelcules
Total (without water)12,9222
Polymers12,9222
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 #5closest to the average

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Components

#1: Protein/peptide high mobility group box transcription factor 1


Mass: 2578.901 Da / Num. of mol.: 1 / Fragment: Sin3 Interaction Domain, Residues 6 to 21 / Source method: obtained synthetically
Details: The peptide sequence was synthesized using automated methods. The sequence is naturally found in Mus musculus (mouse).
References: UniProt: Q8BUS3, UniProt: Q8R316*PLUS
#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
1223D 13C-separated NOESY
1322D double half-filtered NOESY
1423D 13C-filtered,13C-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM 1:1 SID UNLABELED, PAH2 U-15N90% H2O/10% D2O
21.4 mM 1:1 SID UNLABELED, PAH2 U-15N,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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