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- PDB-1e91: Structure of the complex of the Mad1-Sin3B interaction domains -

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Basic information

Entry
Database: PDB / ID: 1.0E+91
TitleStructure of the complex of the Mad1-Sin3B interaction domains
Components
  • MAD PROTEIN (MAX DIMERIZER)
  • PAIRED AMPHIPATHIC HELIX PROTEIN SIN3B
KeywordsEUKARYOTIC TRANSCRIPTIONAL REGULATION / SIN3 / PAH DOMAINS / MAD1 / 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 / Y chromosome / X chromosome / histone deacetylase complex ...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 / Y chromosome / X chromosome / histone deacetylase complex / 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 / cytoplasm / cytosol
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)
HOMO SAPIENS (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, ITERATIVE NOE-ASSIGNMENT
AuthorsSpronk, C.A.E.M. / Tessari, M. / Kaan, A.M. / Jansen, J.F.A. / Vermeulen, M. / Stunnenberg, H.G. / Vuister, G.W.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The MAD1-Sin3B Interaction Involves a Novel Helical Fold
Authors: Spronk, C.A.E.M. / Tessari, M. / Kaan, A.M. / Jansen, J.F.A. / Vermeulen, M. / Stunnenberg, H.G. / Vuister, G.W.
History
DepositionOct 4, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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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: MAD PROTEIN (MAX DIMERIZER)


Theoretical massNumber of molelcules
Total (without water)11,6202
Polymers11,6202
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 / 10030 STRUCTURES WITH NO RESTRAINT VIOLATIONS, 20 LOWEST ENERGY STRUCTURES FINALLY SELECTED
RepresentativeModel #1

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Components

#1: Protein PAIRED AMPHIPATHIC HELIX PROTEIN SIN3B


Mass: 10097.263 Da / Num. of mol.: 1 / Fragment: PAH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Gene: SIN3B / Plasmid: PGEX2T / Gene (production host): SIN3B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q62141
#2: Protein/peptide MAD PROTEIN (MAX DIMERIZER)


Mass: 1522.719 Da / Num. of mol.: 1 / Fragment: SIN INTERACTION DOMAIN / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q05195

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-NOESY-HSQC
12115N-NOESY-HSQC
13115N-HMQC-NOESY-HSQC
141(13C-FILTERED)-NOESY- (13C-EDITED)-HSQC
151HNCA
161HNCO
171HN(CO)CA
181CBCA(CO)NNH
191HN(CA)CB
1101(H)CCH-TOCSY
1111(13C/15N-FILTERED)-NOESY
1121(13C/15N-FILTERED)-TOCSY
1131HNHA
1141HBHA(CBCACO)NNH

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Sample preparation

Sample conditionspH: 6.3 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGER, A.T. ET ALrefinement
ARIAARIAstructure solution
RefinementMethod: SIMULATED ANNEALING, ITERATIVE NOE-ASSIGNMENT / Software ordinal: 1
Details: STRUCTURES WERE REFINED USING THE PROGRAM ARIA 1.0 (NILGES ET AL) FOR ITERATIVE NOE ASSIGNMENT.
NMR ensembleConformer selection criteria: 30 STRUCTURES WITH NO RESTRAINT VIOLATIONS, 20 LOWEST ENERGY STRUCTURES FINALLY SELECTED
Conformers calculated total number: 100 / Conformers submitted total number: 20

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