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- PDB-1xc5: Solution Structure of the SMRT Deacetylase Activation Domain -

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Basic information

Entry
Database: PDB / ID: 1xc5
TitleSolution Structure of the SMRT Deacetylase Activation Domain
ComponentsNuclear receptor corepressor 2
KeywordsTRANSCRIPTION COREPRESSOR / four-helix structure / three-helix triangle
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / estrous cycle / Regulation of MECP2 expression and activity / nuclear retinoid X receptor binding ...Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / estrous cycle / Regulation of MECP2 expression and activity / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to organonitrogen compound / transcription repressor complex / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / histone deacetylase binding / transcription corepressor activity / response to estradiol / nuclear body / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus
Similarity search - Function
N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily ...N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Simulated annealing protocol
AuthorsCodina, A. / Love, J.D. / Li, Y. / Lazar, M.A. / Neuhaus, D. / Schwabe, J.W.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural insights into the interaction and activation of histone deacetylase 3 by nuclear receptor corepressors
Authors: Codina, A. / Love, J.D. / Li, Y. / Lazar, M.A. / Neuhaus, D. / Schwabe, J.W.R.
History
DepositionSep 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor corepressor 2


Theoretical massNumber of molelcules
Total (without water)8,5791
Polymers8,5791
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)28 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nuclear receptor corepressor 2 / SMRT / N-CoR2 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRTe / Thyroid- ...SMRT / N-CoR2 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRTe / Thyroid- / retinoic-acid-receptor-associated corepressor / T3 receptor- associating factor / TRAC / CTG repeat protein 26 / SMAP270


Mass: 8578.959 Da / Num. of mol.: 1 / Fragment: Deacetylase Activation Domain (residues 410-480)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9Y618

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
112DQF-COSY
122DQ-correlation
1312D TOCSY
1412D NOESY
1533D 15N-separated TOCSY
1633D 15N-separated NOESY
NMR detailsText: This structure was determined using a combination of standard 2D homonuclear techniques and 3D 15N TOCSY-HSQC and 15N NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2mM DAD, 50mM NaCl, 50mM phosphate buffer NA93% H2O/7% D2O
21-2mM DAD, 50mM NaCl, 50mM phosphate buffer NA100% D2O
31-2mM DAD U-15N, 50mM NaCl, 50mM phosphate buffer NA93% H2O/7% D2O
Sample conditionsIonic strength: 0.35 M / pH: 6.8 / Pressure: ambient / Temperature: 290 K

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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
Bruker AVANCEBrukerAVANCE8001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker GmbH, Karlsruhe, Germanyprocessing
NMRPipe02/2000Frank Delaglio Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer, Ad Baxprocessing
Sparky3.106T.D. Goddard, D.G. Knellerdata analysis
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: Simulated annealing protocol / Software ordinal: 1 / Details: supplied with the program CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 28

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