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- PDB-2ltp: Solution structure of the SANT2 domain of the human nuclear recep... -

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Basic information

Entry
Database: PDB / ID: 2ltp
TitleSolution structure of the SANT2 domain of the human nuclear receptor corepressor 2 (NCoR2), Northeast Structural Genomics Consortium (NESG) target ID HR4636E
ComponentsNuclear receptor corepressor 2
KeywordsTranscription regulator / SMRT / TRAC / SGC / Structural Genomics Consortium / NESG / Northeast Structural Genomics Consortium / PSI-Biology
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 / Regulation of MECP2 expression and activity / estrous cycle / 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 / Regulation of MECP2 expression and activity / estrous cycle / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / : / 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 / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / HCMV Early Events / 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 ...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 / restrained molecular dynamics
Model detailsfewest violations, model 1
AuthorsMontecchio, M. / Lemak, A. / Yee, A. / Xu, C. / Garcia, M. / Houliston, S. / Bellanda, M. / Min, J. / Montelione, G.T. / Arrowsmith, C. ...Montecchio, M. / Lemak, A. / Yee, A. / Xu, C. / Garcia, M. / Houliston, S. / Bellanda, M. / Min, J. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Solution structure of the SANT2 domain of the human nuclear receptor corepressor 2 (NCoR2).
Authors: Montecchio, M. / Lemak, A. / Yee, A. / Xu, C. / Garcia, M. / Houliston, S. / Bellanda, M. / Min, J. / Montelione, G.T. / Arrowsmith, C.
History
DepositionMay 30, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)10,7761
Polymers10,7761
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 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

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


Mass: 10776.375 Da / Num. of mol.: 1 / Fragment: SANT 2 domain residues 615-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOR2, CTG26 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y618

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HBHA(CO)NH
1613D 1H-15N NOESY
1712D 1H-13C HSQC aliphatic
1812D 1H-13C HSQC aromatic
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic
11113D (H)CCH-TOCSY
11213D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] protein 1, 25 mM sodium phosphate, 200 mM NaCl, 0.01 mM ZnSO4, 10 mM DTT, 1 mM benzamidine, 0.01 % NaN3, 95 % H2O, 5 % D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity 1-1[U-13C; U-15N]1
25 mMsodium phosphate-21
200 mMNaCl-31
0.01 mMZnSO4-41
10 mMDTT-51
1 mMbenzamidine-61
0.01 %NaN3-71
95 %H2O-81
5 %D2O-91
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardpeak picking
MDDGUIGutmanas A., Orekhov V.processing
FMCGUILemak A., Steren C., Llinas M., Arrowsmith C.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVSBhattacharya and Montelionestructure validation
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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