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- PDB-5aj1: Solution Structure of the Smarc Domain -

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Basic information

Entry
Database: PDB / ID: 5aj1
TitleSolution Structure of the Smarc Domain
ComponentsSWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / brahma complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Formation of the embryonic stem cell BAF (esBAF) complex / npBAF complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / brahma complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Formation of the embryonic stem cell BAF (esBAF) complex / npBAF complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / regulation of G0 to G1 transition / Tat protein binding / RNA polymerase I preinitiation complex assembly / XY body / host-mediated activation of viral transcription / regulation of nucleotide-excision repair / nucleosome disassembly / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of myoblast differentiation / regulation of G1/S transition of mitotic cell cycle / transcription initiation-coupled chromatin remodeling / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / DNA integration / fibrillar center / kinetochore / nuclear matrix / RMTs methylate histone arginines / p53 binding / nervous system development / transcription coactivator activity / chromatin remodeling / regulation of transcription by RNA polymerase II / nucleolus / chromatin / 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 / CNS
AuthorsAllen, M.D. / Freund, S.M.V. / Zinzalla, G. / Bycroft, M.
CitationJournal: Structure / Year: 2015
Title: The Swi/Snf Subunit Ini1 Contains an N-Terminal Winged Helix DNA Binding Domain that is a Target for Mutations in Schwannomatosis.
Authors: Allen, M.D. / Freund, S.M.V. / Zinzalla, G. / Bycroft, M.
History
DepositionFeb 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Atomic model
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 19, 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: SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1


Theoretical massNumber of molelcules
Total (without water)12,9961
Polymers12,9961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20NO VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein 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 / SMARC B1 DOMAIN


Mass: 12995.907 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GGS AT THE N-TERMINUS RESULTS FROM A TEV CLEAVAGE SITE.
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q12824
Sequence detailsGGS AT THE N-TERMINUS RESULTS FROM A TEV PROTEASE CLEAVAGE SITE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
141HSQC
151HN(CA)CB
161CBCA(CO)NH
171HNCO
181HN(CA)CO
191HNHB
NMR detailsText: THE DOMAIN WAS ASSIGNED USING 13C, 15N-LABELED PROTEIN AND THE STRUCTURE WAS DETERMINED USING UNLABELLED PROTEIN.

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Sample preparation

DetailsContents: 95% WATER/5% D2O
Sample conditionsIonic strength: 100 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 293.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE, JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON, WARRENrefinement
ANSIGstructure solution
CNSstructure solution
RefinementMethod: CNS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NO VIOLATIONS / Conformers calculated total number: 20 / Conformers submitted total number: 20

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