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- PDB-1g1e: NMR STRUCTURE OF THE HUMAN MAD1 TRANSREPRESSION DOMAIN SID IN COM... -

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Basic information

Entry
Database: PDB / ID: 1g1e
TitleNMR STRUCTURE OF THE HUMAN MAD1 TRANSREPRESSION DOMAIN SID IN COMPLEX WITH MAMMALIAN SIN3A PAH2 DOMAIN
Components
  • MAD1 PROTEIN
  • SIN3A
KeywordsTRANSCRIPTION / Four-helix bundle / Protein-peptide Complex
Function / homology
Function and homology information


cellular response to tert-butyl hydroperoxide / Regulation of MECP2 expression and activity / Mad-Max complex / response to methylglyoxal / SUMOylation of transcription cofactors / regulation of hormone levels / 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 ...cellular response to tert-butyl hydroperoxide / Regulation of MECP2 expression and activity / Mad-Max complex / response to methylglyoxal / SUMOylation of transcription cofactors / regulation of hormone levels / 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 / transcription regulator inhibitor activity / regulation of axon extension / 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 / : / positive regulation of G2/M transition of mitotic cell cycle / activation of innate immune response / transcription repressor complex / positive regulation of neuron differentiation / negative regulation of cell migration / cellular response to glucose stimulus / negative regulation of transforming growth factor beta receptor signaling pathway / protein localization / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / rhythmic process / DNA replication / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / 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 / protein-containing complex binding / regulation of DNA-templated transcription / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / 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 Sin3a
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model type detailsminimized average
AuthorsBrubaker, K. / Cowley, S.M. / Huang, K. / Eisenman, R.N. / Radhakrishnan, I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Solution structure of the interacting domains of the Mad-Sin3 complex: implications for recruitment of a chromatin-modifying complex.
Authors: Brubaker, K. / Cowley, S.M. / Huang, K. / Loo, L. / Yochum, G.S. / Ayer, D.E. / Eisenman, R.N. / Radhakrishnan, I.
History
DepositionOct 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAD1 PROTEIN
B: SIN3A


Theoretical massNumber of molelcules
Total (without water)12,3122
Polymers12,3122
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)15 / 25structures with favorable non-bond energy,structures with the least restraint violations
RepresentativeModel #15minimized average structure

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Components

#1: Protein/peptide MAD1 PROTEIN / MAX DIMERIZATION PROTEIN


Mass: 1968.302 Da / Num. of mol.: 1
Fragment: SIN3 INTERACTION DOMAIN (SID) TRANSREPRESSION DOMAIN
Source method: obtained synthetically
Details: The peptide sequence was synthesized via automated methods. The sequence is naturally found in Homo sapiens (human).
References: GenBank: 4505069, UniProt: Q05195*PLUS
#2: Protein SIN3A


Mass: 10343.438 Da / Num. of mol.: 1 / Fragment: PAIRED AMPHIPATHIC HELIX 2 (PAH2 REPEAT)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET24 / 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 15N-separated NOESY
121HNHA
1322D 13C,15N-double-half-filtered NOESY
1422D 13C-double-half-filtered NOESY
1533D 13C-separated NOESY
1633D HACAHB
1732D Spin-echo Difference for JNCgamma, JC'Cgamma
1813D HNHB
NMR detailsText: Interproton NOEs were assigned iteratively but manually during structure refinement.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM 1:1 SID unlabeled, PAH2 U-15N; 1.6 mM 1:1 SID unlabeled, PAH2 U-15N, U-13C.90% H2O/10% D2O
21.6 mM 1:1 SID unlabeled, PAH2 U-15N,13C; 20 mM phosphate buffer pH 6.0, 0.2% NaN390% H2O/10% D2O
31.6 mM 1:1 SID unlabeled, PAH2 U-15N,13C; 20 mM phosphate buffer pH 6.0, 0.2% NaN3100% D2O
Sample conditionsIonic strength: 20 mM phosphate / pH: 6.0 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
Felix98Molecular Simulationsprocessing
Felix98Molecular Simulationsdata analysis
DYANA1.5Guntert, Wuthrichstructure solution
CNS1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on 1612 unique distance constraints, 198 torsion angle constraints and 72 JHNHA coupling constant constraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with favorable non-bond energy,structures with the least restraint violations
Conformers calculated total number: 25 / Conformers submitted total number: 15

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