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- PDB-6uch: SMARCB1 nucleosome-interacting C-terminal alpha helix -

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Basic information

Entry
Database: PDB / ID: 6uch
TitleSMARCB1 nucleosome-interacting C-terminal alpha helix
ComponentsSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
KeywordsNUCLEAR PROTEIN / mSWI-SNF complex / BAF complex / Chromatin Remodeling / SMARCB1 / BAF47 / Positive charge cluster / Arginine cluster / Nucleosome Binding / Alpha Helix
Function / homology
Function and homology information


single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / blastocyst hatching / regulation of G0 to G1 transition ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / blastocyst hatching / regulation of G0 to G1 transition / hepatocyte differentiation / regulation of nucleotide-excision repair / RSC-type complex / XY body / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / germ cell nucleus / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / positive regulation of DNA-binding transcription factor activity / kinetochore / fibrillar center / RMTs methylate histone arginines / DNA integration / nuclear matrix / p53 binding / nervous system development / transcription coactivator activity / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / SWI/SNF Subunit INI1, DNA binding domain / Chromatin-remodeling complex component Sfh1/SNF5 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1
Similarity search - Domain/homology
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsValencia, A.M. / Sun, Z.Y.J. / Seo, H.S. / Vangos, H.S. / Yeoh, Z.C. / Mashtalir, N. / Dhe-Paganon, S. / Kadoch, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Cell / Year: 2019
Title: Recurrent SMARCB1 Mutations Reveal a Nucleosome Acidic Patch Interaction Site That Potentiates mSWI/SNF Complex Chromatin Remodeling.
Authors: Valencia, A.M. / Collings, C.K. / Dao, H.T. / St Pierre, R. / Cheng, Y.C. / Huang, J. / Sun, Z.Y. / Seo, H.S. / Mashtalir, N. / Comstock, D.E. / Bolonduro, O. / Vangos, N.E. / Yeoh, Z.C. / ...Authors: Valencia, A.M. / Collings, C.K. / Dao, H.T. / St Pierre, R. / Cheng, Y.C. / Huang, J. / Sun, Z.Y. / Seo, H.S. / Mashtalir, N. / Comstock, D.E. / Bolonduro, O. / Vangos, N.E. / Yeoh, Z.C. / Dornon, M.K. / Hermawan, C. / Barrett, L. / Dhe-Paganon, S. / Woolf, C.J. / Muir, T.W. / Kadoch, C.
History
DepositionSep 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 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: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)4,7481
Polymers4,7481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / BRG1-associated factor 47 / BAF47 / Integrase interactor 1 protein / SNF5 homolog / hSNF5


Mass: 4748.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCB1, BAF47, INI1, SNF5L1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12824

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D HN(CO)CA
151isotropic13D HN(CA)CO
161isotropic13D C(CO)NH
1101isotropic13D H(CCO)NH
191isotropic13D 1H-15N NOESY
182isotropic12D NOESY
172isotropic12D TOCSY
1121isotropic12D 1H-15N HSQC
1111isotropic12D 1H-13C HSQC aliphatic
1131isotropic12D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM [U-100% 13C; U-100% 15N] SMARCB1CC, 137 mM NaCl, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 90% H2O/10% D2O15N13C-SMARCB1CC90% H2O/10% D2O
solution2230 uM SMARCB1CC, 137 mM NaCl, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 100% D2Ounlabeled-SMARCB1CC100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMSMARCB1CC[U-100% 13C; U-100% 15N]1
137 mMNaClnatural abundance1
2.7 mMpotassium chloridenatural abundance1
10 mMNa2HPO4natural abundance1
1.8 mMKH2PO4natural abundance1
230 uMSMARCB1CCnatural abundance2
137 mMNaClnatural abundance2
2.7 mMpotassium chloridenatural abundance2
10 mMNa2HPO4natural abundance2
1.8 mMKH2PO4natural abundance2
Sample conditionsIonic strength: 150 mM / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 700 MHz / Details: cryogenic probe

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
hmsISTHyberts and Wagnerprocessing
CARAKeller and Wuthrichdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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