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- PDB-2ld7: Solution structure of the mSin3A PAH3-SAP30 SID complex -

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Basic information

Entry
Database: PDB / ID: 2ld7
TitleSolution structure of the mSin3A PAH3-SAP30 SID complex
Components
  • Histone deacetylase complex subunit SAP30
  • Paired amphipathic helix protein Sin3a
KeywordsTRANSCRIPTION
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 / HDACs deacetylate histones / 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 / response to methylglyoxal / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / SUMOylation of transcription cofactors / regulation of hormone levels / HDACs deacetylate histones / 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 / 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 / skeletal muscle cell differentiation / hematopoietic progenitor cell differentiation / transcription regulator inhibitor activity / positive regulation of defense response to virus by host / positive regulation of G2/M transition of mitotic cell cycle / transcription repressor complex / positive regulation of neuron differentiation / activation of innate immune response / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / cellular response to glucose stimulus / kinetochore / transcription corepressor activity / rhythmic process / intracellular protein localization / heterochromatin formation / 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 / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #20 / Histone deacetylase complex subunit SAP30 zinc-finger / SAP30 zinc-finger / Histone deacetylase complex subunit SAP30/SAP30-like / Histone deacetylase complex subunit SAP30, Sin3 binding domain / SAP30, C-terminal domain superfamily / Sin3 binding region of histone deacetylase complex subunit SAP30 / Paired amphipathic helix / Paired amphipathic helix 2 (pah2 repeat) ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #20 / Histone deacetylase complex subunit SAP30 zinc-finger / SAP30 zinc-finger / Histone deacetylase complex subunit SAP30/SAP30-like / Histone deacetylase complex subunit SAP30, Sin3 binding domain / SAP30, C-terminal domain superfamily / Sin3 binding region of histone deacetylase complex subunit SAP30 / 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 non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone deacetylase complex subunit SAP30 / Paired amphipathic helix protein Sin3a
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsXie, T. / He, Y. / Korkeamaki, H. / Zhang, Y. / Imhoff, R. / Lohi, O. / Radhakrishnan, I.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of the 30-kDa Sin3-associated protein (SAP30) in complex with the mammalian Sin3A corepressor and its role in nucleic acid binding.
Authors: Xie, T. / He, Y. / Korkeamaki, H. / Zhang, Y. / Imhoff, R. / Lohi, O. / Radhakrishnan, I.
History
DepositionMay 16, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650 HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase complex subunit SAP30
B: Paired amphipathic helix protein Sin3a


Theoretical massNumber of molelcules
Total (without water)19,2212
Polymers19,2212
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 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Histone deacetylase complex subunit SAP30 / 30 kDa Sin3-associated polypeptide / Sin3 corepressor complex subunit SAP30 / Sin3-associated polypeptide p30


Mass: 10546.753 Da / Num. of mol.: 1 / Fragment: Interaction with SIN3A region residues 130-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sap30 / Production host: Escherichia coli (E. coli) / References: UniProt: O88574
#2: Protein Paired amphipathic helix protein Sin3a / Histone deacetylase complex subunit Sin3a / Transcriptional corepressor Sin3a


Mass: 8673.931 Da / Num. of mol.: 1 / Fragment: PAH 3 domain residues 456-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sin3a, Kiaa4126 / 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
1223D 1H-15N NOESY
1333D 1H-13C NOESY aliphatic
1443D 1H-13C NOESY aliphatic
1512D 1H-15N HSQC
1622D 1H-15N HSQC
1713D CBCA(CO)NH
1823D CBCA(CO)NH
1913D HN(CA)CB
11023D HN(CA)CB
11113D HNCO
11223D HNCO
11313D HNCA
11423D HNCA
11533D (H)CCH-COSY
11643D (H)CCH-COSY
11733D (H)CCH-TOCSY
11843D (H)CCH-TOCSY
11932D 1H-13C HSQC aromatic
12042D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] protein 1, 1 mM protein 2, 90% H2O/10% D2O90% H2O/10% D2O
21 mM protein 1, 1 mM [U-100% 13C; U-100% 15N] protein 2, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] protein 1, 1 mM protein 2, 100% D2O100% D2O
41 mM protein 1, 1 mM [U-100% 13C; U-100% 15N] protein 2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein_1-1[U-100% 13C; U-100% 15N]1
1 mMprotein_2-21
1 mMprotein_1-32
1 mMprotein_2-4[U-100% 13C; U-100% 15N]2
1 mMprotein_1-5[U-100% 13C; U-100% 15N]3
1 mMprotein_2-63
1 mMprotein_1-74
1 mMprotein_2-8[U-100% 13C; U-100% 15N]4
Sample conditionspH: 6.5 / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Felix98Accelrys Software Inc.processing
VnmrJVariancollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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