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- PDB-6sy2: Structure of the BRK domain of the SWI/SNF chromatin remodelling ... -

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Basic information

Entry
Database: PDB / ID: 6sy2
TitleStructure of the BRK domain of the SWI/SNF chromatin remodelling complex subunit BRG1 reveals a potential role in protein-protein interactions
ComponentsTranscription activator BRG1
KeywordsUNKNOWN FUNCTION / BRG1 / BRK domain / SWI/SNF / chromatin remodelling
Function / homology
Function and homology information


chromatin remodeling => GO:0006338 / positive regulation of glucose mediated signaling pathway / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / nBAF complex / GBAF complex / neural retina development ...chromatin remodeling => GO:0006338 / positive regulation of glucose mediated signaling pathway / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / nBAF complex / GBAF complex / neural retina development / regulation of G0 to G1 transition / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / ATP-dependent chromatin remodeler activity / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear androgen receptor binding / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / Interleukin-7 signaling / helicase activity / transcription coregulator binding / positive regulation of cell differentiation / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lysine-acetylated histone binding / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / positive regulation of DNA-binding transcription factor activity / nuclear matrix / positive regulation of miRNA transcription / transcription corepressor activity / p53 binding / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / hydrolase activity / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular space / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
Ribosomal Protein L9; domain 1 - #120 / SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Ribosomal Protein L9; domain 1 / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ ...Ribosomal Protein L9; domain 1 - #120 / SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Ribosomal Protein L9; domain 1 / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription activator BRG1 / Transcription activator BRG1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAllen, M.D. / Bycoft, M. / Zinzalla, G.
CitationJournal: Protein Sci. / Year: 2020
Title: Structure of the BRK domain of the SWI/SNF chromatin remodeling complex subunit BRG1 reveals a potential role in protein-protein interactions.
Authors: Allen, M.D. / Bycroft, M. / Zinzalla, G.
History
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription activator BRG1


Theoretical massNumber of molelcules
Total (without water)5,2881
Polymers5,2881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4120 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1none

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Components

#1: Protein/peptide Transcription activator BRG1


Mass: 5287.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4 / Plasmid: HLTV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A2R8Y7S2, UniProt: P51532*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D NOESY
122isotropic12D TOCSY
132isotropic12D DQF-COSY
141isotropic23D HN(CA)CB
151isotropic23D CBCA(CO)NH
1111isotropic23D HNCO
1101isotropic23D HN(CA)CO
191isotropic23D HBHA(CO)NH
181isotropic22D 1H-15N HSQC
171isotropic22D 1H-13C HSQC
163isotropic22D 1H-13C HSQC aliphatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-99% 13C; U-99% 15N] BRG1 BRK domain, 90% H2O/10% D2O20mM potassium phosphate, pH 6.5 150mM NaCl13C, 15N sample90% H2O/10% D2O
solution22 mM unlabelled BRG1 BRK domain, 90% H2O/10% D2O20mM potassium phosphate, pH 6.5 150mM NaClunlabelled90% H2O/10% D2O
solution31 mM [U-10% 13C] BRG1 BRK domain, 90% H2O/10% D2O20mM potassium phosphate, pH 6.5 150mM NaCl10% C sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBRG1 BRK domain[U-99% 13C; U-99% 15N]1
2 mMBRG1 BRK domainunlabelled2
1 mMBRG1 BRK domain[U-10% 13C]3
Sample conditionsDetails: 20mM potassium phosphate pH 6.5 100mM NaCl / Ionic strength: 140 mM / Label: Standard conditions / pH: 6.5 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 293 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE8001All homonuclear experiments
Bruker AVANCEBrukerAVANCE6002All heteronuclear experiments

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ANSIGKraulischemical shift assignment
AzaraBoucherprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: none
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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