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- PDB-1pd7: Extended SID of Mad1 bound to the PAH2 domain of mSin3B -

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Basic information

Entry
Database: PDB / ID: 1pd7
TitleExtended SID of Mad1 bound to the PAH2 domain of mSin3B
Components
  • Mad1
  • Sin3b protein
KeywordsTRANSCRIPTION / PAH2 / SIN3 / MAD1 / EUKARYOTIC TRANSCRIPTIONAL REGULATION / PROTEIN-PROTEIN INTERACTIONS
Function / homology
Function and homology information


autosome / Mad-Max complex / 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 ...autosome / Mad-Max complex / 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 / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Max dimerization protein 1 / 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 ...Max dimerization protein 1 / 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-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Max dimerization protein 1 / Paired amphipathic helix protein Sin3b
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, ITERATIVE NOE-ASSIGNMENT
AuthorsVan Ingen, H. / Lasonder, E. / Jansen, J.F. / Kaan, A.M. / Spronk, C.A. / Stunnenberg, H.G. / Vuister, G.W.
CitationJournal: Biochemistry / Year: 2004
Title: Extension of the binding motif of the sin3 interacting domain of the mad family proteins(,).
Authors: Van Ingen, H. / Lasonder, E. / Jansen, J.F. / Kaan, A.M. / Spronk, C.A. / Stunnenberg, H.G. / Vuister, G.W.
History
DepositionMay 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sin3b protein
B: Mad1


Theoretical massNumber of molelcules
Total (without water)13,0762
Polymers13,0762
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)30 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sin3b protein


Mass: 10097.263 Da / Num. of mol.: 1 / Fragment: PAH2 domain (residues 148-232)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SIN3 / Plasmid: PGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): PBL21 / References: UniProt: Q62141
#2: Protein/peptide Mad1 /


Mass: 2978.386 Da / Num. of mol.: 1 / Fragment: extended SID domain (residues 5-28) / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: Q05195

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D X-filtered NOESY
1413D 13C-edited-13C-filtered HMQC-NOESY
1513D 15N-edited-15N-filtered HSQC-NOESY
NMR detailsText: A collection of PDB files, compiled by NMR_REFINE

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Sample preparation

DetailsContents: 1.3 mM PAH2 U-15,13C; 1.3 mM SID 50 mM phosphate buffer pH 6.3 trace amounts of NaN3 and Pefabloc
Solvent system: 95% H20, 5% D20
Sample conditionsIonic strength: 50 mM K2HPO4/KH2PO4 / pH: 6.3 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2002Delaglioprocessing
XEASY1.3.9Bartelsdata analysis
X-PLOR3.581Brungerstructure solution
X-PLOR3.581Brungerrefinement
RefinementMethod: simulated annealing, ITERATIVE NOE-ASSIGNMENT / 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: 30

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