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- PDB-2n2h: Solution structure of Sds3 in complex with Sin3A -

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Basic information

Entry
Database: PDB / ID: 2n2h
TitleSolution structure of Sds3 in complex with Sin3A
Components
  • Paired amphipathic helix protein Sin3a
  • Sin3 histone deacetylase corepressor complex component SDS3
KeywordsTranscription / protein binding / transcription repression / corepressor complex / histone deacetylase complex
Function / homology
Function and homology information


Regulation of MECP2 expression and activity / HDACs deacetylate histones / response to methylglyoxal / SUMOylation of transcription cofactors / regulation of hormone levels / cerebral cortex neuron differentiation / blastocyst hatching / negative regulation of circadian rhythm / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of lipid metabolism by PPARalpha ...Regulation of MECP2 expression and activity / HDACs deacetylate histones / response to methylglyoxal / SUMOylation of transcription cofactors / regulation of hormone levels / cerebral cortex neuron differentiation / blastocyst hatching / 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 / Ub-specific processing proteases / cellular response to dopamine / regulation of axon extension / transcription regulator inhibitor activity / negative regulation of protein localization to nucleus / Sin3-type complex / positive regulation of stem cell population maintenance / 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 / positive regulation of neuron differentiation / transcription repressor complex / 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 / protein localization / kinetochore / histone deacetylase binding / transcription corepressor activity / rhythmic process / in utero embryonic development / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA replication / nuclear body / chromatin remodeling / negative regulation of DNA-templated transcription / apoptotic process / 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 / enzyme binding / protein-containing complex / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Sds3-like / Sds3-like / Sds3-like / 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 ...Sds3-like / Sds3-like / Sds3-like / 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.
Similarity search - Domain/homology
Paired amphipathic helix protein Sin3a / Sin3 histone deacetylase corepressor complex component SDS3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsClark, M. / Radhakrishnan, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex.
Authors: Clark, M.D. / Marcum, R. / Graveline, R. / Chan, C.W. / Xie, T. / Chen, Z. / Ding, Y. / Zhang, Y. / Mondragon, A. / David, G. / Radhakrishnan, I.
History
DepositionMay 8, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sin3 histone deacetylase corepressor complex component SDS3
B: Paired amphipathic helix protein Sin3a


Theoretical massNumber of molelcules
Total (without water)17,8242
Polymers17,8242
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-15 kcal/mol
Surface area10720 Å2
MethodPISA
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 Sin3 histone deacetylase corepressor complex component SDS3 / Suppressor of defective silencing 3 protein homolog


Mass: 3125.531 Da / Num. of mol.: 1 / Fragment: UNP residues 205-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Suds3, Sds3 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BR65
#2: Protein Paired amphipathic helix protein Sin3a / Histone deacetylase complex subunit Sin3a / Transcriptional corepressor Sin3a


Mass: 14698.822 Da / Num. of mol.: 1 / Fragment: UNP residues 608-729
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sin3a, Kiaa4126 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / 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-15N NOESY
1213D 1H-13C NOESY
1323D 1H-15N NOESY
1423D 1H-13C NOESY
1513D CBCA(CO)NH
1613D HN(CA)CB
1723D CBCA(CO)NH
1823D HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 13C; U-100% 15N] Sin3HID, 0.5-1 mM Sds3SID, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 13C; U-100% 15N] Sds3SID, 0.5-1 mM Sin3HID, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSin3HID-1[U-100% 13C; U-100% 15N]0.5-11
mMSds3SID-20.5-11
mMSds3SID-3[U-100% 13C; U-100% 15N]0.5-12
mMSin3HID-40.5-12
Sample conditionsIonic strength: 0.12 / pH: 6.7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
CNSBrunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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