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- PDB-7sxi: Solution Structure of Sds3 Capped Tudor Domain -

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Basic information

Entry
Database: PDB / ID: 7sxi
TitleSolution Structure of Sds3 Capped Tudor Domain
ComponentsSin3 histone deacetylase corepressor complex component SDS3
KeywordsGENE REGULATION / Transcriptional corepressor / Tudor domain / Nucleic acid binding / G-quadruplex binding
Function / homology
Function and homology information


HDACs deacetylate histones / blastocyst hatching / negative regulation of stem cell population maintenance / Ub-specific processing proteases / Sin3-type complex / positive regulation of stem cell population maintenance / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / histone deacetylase binding / nuclear body ...HDACs deacetylate histones / blastocyst hatching / negative regulation of stem cell population maintenance / Ub-specific processing proteases / Sin3-type complex / positive regulation of stem cell population maintenance / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / histone deacetylase binding / nuclear body / chromatin remodeling / negative regulation of DNA-templated transcription / apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Sds3-like / Sds3-like / Sds3-like
Similarity search - Domain/homology
Sin3 histone deacetylase corepressor complex component SDS3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsMarcum, R.D. / Radhakrishnan, I.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association17GRNT33680167 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: A capped Tudor domain within a core subunit of the Sin3L/Rpd3L histone deacetylase complex binds to nucleic acid G-quadruplexes.
Authors: Marcum, R.D. / Hsieh, J. / Giljen, M. / Justice, E. / Daffern, N. / Zhang, Y. / Radhakrishnan, I.
History
DepositionNov 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sin3 histone deacetylase corepressor complex component SDS3


Theoretical massNumber of molelcules
Total (without water)9,3911
Polymers9,3911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Sin3 histone deacetylase corepressor complex component SDS3 / Suppressor of defective silencing 3 protein homolog


Mass: 9390.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Suds3, Sds3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BR65

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
122isotropic13D 1H-13C NOESY aliphatic
132isotropic12D 1H-1H NOESY
142isotropic13D CBCA(CO)NH
152isotropic13D HN(CA)CB
182isotropic13D (H)CCH-COSY
172isotropic13D (H)CCH-TOCSY
162isotropic13D C(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.35 mM [U-100% 15N] Sds3 CTD, 90% H2O/10% D2O15N-labeled sample15N_sample90% H2O/10% D2O
solution20.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O15N,13C-labeled sample15N13C_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMSds3 CTD[U-100% 15N]1
0.35 mMSds3 CTD[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.07 M / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent Direct Drive / Manufacturer: Agilent / Model: Direct Drive / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
FelixAccelrys Software Inc.processing
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRFAM-SPARKYLee W, Tonelli M, Markley JL. Bioinformatics. 2015 Apr 15; 31(8):1325-7.chemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JL. Bioinformatics. 2015 Apr 15; 31(8):1325-7.peak picking
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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