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- PDB-2czy: Solution structure of the NRSF/REST-mSin3B PAH1 complex -

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Basic information

Entry
Database: PDB / ID: 2czy
TitleSolution structure of the NRSF/REST-mSin3B PAH1 complex
Components
  • Paired amphipathic helix protein Sin3b
  • transcription factor REST (version 3)
KeywordsGENE REGULATION / NRSF / Sin3 / PAH1 / transcriptional repressor
Function / homology
Function and homology information


negative regulation of dense core granule biogenesis / negative regulation of amniotic stem cell differentiation / autosome / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / negative regulation of transcription regulatory region DNA binding / modification of synaptic structure / Regulation of NPAS4 gene transcription / cellular response to electrical stimulus / negative regulation of mesenchymal stem cell differentiation ...negative regulation of dense core granule biogenesis / negative regulation of amniotic stem cell differentiation / autosome / negative regulation of aldosterone biosynthetic process / negative regulation of cortisol biosynthetic process / negative regulation of transcription regulatory region DNA binding / modification of synaptic structure / Regulation of NPAS4 gene transcription / cellular response to electrical stimulus / negative regulation of mesenchymal stem cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of lipid metabolism by PPARalpha / detection of mechanical stimulus involved in sensory perception of sound / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / Cytoprotection by HMOX1 / neuronal stem cell population maintenance / XY body / NGF-stimulated transcription / cardiac muscle tissue development / nervous system process / auditory receptor cell stereocilium organization / positive regulation of programmed cell death / cellular response to glucocorticoid stimulus / regulation of osteoblast differentiation / regulation of alternative mRNA splicing, via spliceosome / positive regulation of stem cell population maintenance / Sin3-type complex / Y chromosome / X chromosome / somatic stem cell population maintenance / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / neuromuscular process controlling balance / negative regulation of cell cycle / negative regulation of neuron differentiation / negative regulation of insulin secretion / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / hematopoietic progenitor cell differentiation / skeletal muscle tissue development / transcription repressor complex / positive regulation of neuron differentiation / negative regulation of cell migration / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / response to ischemia / HDACs deacetylate histones / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of neurogenesis / transcription corepressor activity / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / transcription cis-regulatory region binding / response to hypoxia / chromatin remodeling / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / 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. / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RE1-silencing transcription factor / Paired amphipathic helix protein Sin3b
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsNomura, M. / Uda-Tochio, H. / Murai, K. / Mori, N. / Nishimura, Y.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Neural Repressor NRSF/REST Binds the PAH1 Domain of the Sin3 Corepressor by Using its Distinct Short Hydrophobic Helix
Authors: Nomura, M. / Uda-Tochio, H. / Murai, K. / Mori, N. / Nishimura, Y.
History
DepositionJul 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Paired amphipathic helix protein Sin3b
B: transcription factor REST (version 3)


Theoretical massNumber of molelcules
Total (without water)10,3542
Polymers10,3542
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Paired amphipathic helix protein Sin3b / Sin3B / Transcriptional corepressor Sin3b / Histone deacetylase complex subunit Sin3b


Mass: 8813.080 Da / Num. of mol.: 1 / Fragment: PAH1 domain (residues 31-107)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sin3B / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62141
#2: Protein/peptide transcription factor REST (version 3) / NRSF/REST


Mass: 1540.822 Da / Num. of mol.: 1 / Fragment: Sin3 interaction domain (residues 43-57) / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: Q13127

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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 X-filtered NOESY
131HNHA
1423D 13C-separated NOESY
1522D X-filtered NOESY
1623D 13C-filtered 13C-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.8mM PAH1 U-15N,13C; 0.5-0.8mM SID; 20mM potassium phosphate buffer95% H2O/5% D2O
20.5-0.8mM PAH1 U-15N,13C; 0.5-0.8mM SID; 20mM potassium phosphate buffer100% D2O
Sample conditionsIonic strength: 20mM potassium phosphate / pH: 7.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerrefinement
NMRPipe2004Delaglioprocessing
NMRView5.0.4Johnsondata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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