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- PDB-5y95: Haddock model of mSIN3B PAH1 domain -

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Basic information

Entry
Database: PDB / ID: 5y95
TitleHaddock model of mSIN3B PAH1 domain
ComponentsPaired amphipathic helix protein Sin3b
KeywordsGENE REGULATION / Haddock model / complex
Function / homology
Function and homology information


autosome / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / XY body / cardiac muscle tissue development / Sin3-type complex / Y chromosome / X chromosome / negative regulation of cell cycle ...autosome / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / XY body / cardiac muscle tissue development / Sin3-type complex / Y chromosome / X chromosome / negative regulation of cell cycle / skeletal muscle tissue development / negative regulation of cell migration / transcription corepressor activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
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
Chem-8TL / Paired amphipathic helix protein Sin3b
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
AuthorsKurita, J. / Hirao, Y. / Nishimura, Y.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: A mimetic of the mSin3-binding helix of NRSF/REST ameliorates abnormal pain behavior in chronic pain models.
Authors: Ueda, H. / Kurita, J.I. / Neyama, H. / Hirao, Y. / Kouji, H. / Mishina, T. / Kasai, M. / Nakano, H. / Yoshimori, A. / Nishimura, Y.
History
DepositionAug 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paired amphipathic helix protein Sin3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0792
Polymers8,6501
Non-polymers4301
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6260 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Paired amphipathic helix protein Sin3b / Histone deacetylase complex subunit Sin3b / Transcriptional corepressor Sin3b


Mass: 8649.608 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sin3b, Kiaa0700 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62141
#2: Chemical ChemComp-8TL / propan-2-yl (3R,6S,9aS)-3-ethyl-8-(3-methylbutyl)-6-(2-methylsulfanylethyl)-4,7-bis(oxidanylidene)-9,9a-dihydro-6H-pyrazino[2,1-c][1,2,4]oxadiazine-1-carboxylate


Mass: 429.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H35N3O5S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 100 uM [U-99% 15N] mSin3B, 100 mM sodium phosphate, 95% H2O/5% DMSO
Label: 15N_sample / Solvent system: 95% H2O/5% DMSO
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uMmSin3B[U-99% 15N]1
100 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKBonvinrefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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