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- PDB-2rt5: Structural insights into the recruitment of SMRT by the co-repres... -

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Basic information

Entry
Database: PDB / ID: 2rt5
TitleStructural insights into the recruitment of SMRT by the co-repressor SHARP under phosphorylative regulation
Components
  • Msx2-interacting protein
  • peptide from Silencing mediator of retinoic acid and thyroid hormone receptor
KeywordsTRANSCRIPTION REGULATOR / SHARP / SPOC domain / SMRT / phosphorylation
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 / RHOBTB1 GTPase cycle / positive regulation of neurogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity ...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 / RHOBTB1 GTPase cycle / positive regulation of neurogenesis / 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 / Notch signaling pathway / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / mRNA 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 / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus
Similarity search - Function
SHARP, RNA recognition motif 1 / SHARP, RNA recognition motif 2 / SHARP, RNA recognition motif 3 / SHARP, RNA recognition motif 4 / : / : / : / Msx2-interacting protein, RAM7 domain / Msx2-interacting protein, MID domain / Msx2-interacting protein, nuclear receptor-interacting domain ...SHARP, RNA recognition motif 1 / SHARP, RNA recognition motif 2 / SHARP, RNA recognition motif 3 / SHARP, RNA recognition motif 4 / : / : / : / Msx2-interacting protein, RAM7 domain / Msx2-interacting protein, MID domain / Msx2-interacting protein, nuclear receptor-interacting domain / Spen paralogue/orthologue C-terminal, metazoa / SPOC domain profile. / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / SPOC-like, C-terminal domain superfamily / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Homeobox-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Msx2-interacting protein / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsMikami, S. / Kanaba, T. / Mishima, M.
CitationJournal: Structure / Year: 2014
Title: Structural insights into the recruitment of SMRT by the corepressor SHARP under phosphorylative regulation.
Authors: Mikami, S. / Kanaba, T. / Takizawa, N. / Kobayashi, A. / Maesaki, R. / Fujiwara, T. / Ito, Y. / Mishima, M.
History
DepositionApr 22, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_spectrometer / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Msx2-interacting protein
B: peptide from Silencing mediator of retinoic acid and thyroid hormone receptor


Theoretical massNumber of molelcules
Total (without water)19,5742
Polymers19,5742
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Msx2-interacting protein / SMART/HDAC1-associated repressor protein / SPEN homolog


Mass: 18471.402 Da / Num. of mol.: 1 / Fragment: SPOC domain, residues 3496-3664
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T58
#2: Protein/peptide peptide from Silencing mediator of retinoic acid and thyroid hormone receptor /


Mass: 1102.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / 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 HN(CA)CO
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D C(CO)NH
1713D H(CCO)NH
1814D HC(CO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY-HSQC
11113D 1H-13C NOESY-HSQC
11212D 1H-13C HSQC
11313D CBCA(CO)NH
11413D HN(CA)CB
11513D C(CO)NH
11613D H(CCO)NH
11713D (H)CCH-TOCSY
11812D 15N filtered 1H NOESY
11913D HNHB
12013D HN(CO)HB
12113D 15N edited NOESY-HSQC
12213D 13C edited NOESY-HSQC

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Sample preparation

DetailsSolvent system: 93% H2O/7% D2O
Sample conditionsIonic strength: 0 / pH: 7.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR softwareName: CNS / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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