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- PDB-1uhr: Solution structure of the SWIB domain of mouse BRG1-associated fa... -

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Entry
Database: PDB / ID: 1uhr
TitleSolution structure of the SWIB domain of mouse BRG1-associated factor 60a
ComponentsSWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily D member 1
KeywordsGENE REGULATION / structural genomics / SWI/SNF / Chromatin remodeling / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Formation of the canonical BAF (cBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RMTs methylate histone arginines / npBAF complex / nBAF complex / regulation of G0 to G1 transition ...Formation of the canonical BAF (cBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RMTs methylate histone arginines / npBAF complex / nBAF complex / regulation of G0 to G1 transition / cellular response to fatty acid / regulation of nucleotide-excision repair / SWI/SNF complex / nucleosome disassembly / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair / negative regulation of cell differentiation / positive regulation of myoblast differentiation / regulation of G1/S transition of mitotic cell cycle / transcription initiation-coupled chromatin remodeling / positive regulation of cell differentiation / transcription coregulator activity / kinetochore / nuclear matrix / nervous system development / molecular adaptor activity / chromatin remodeling / signaling receptor binding / chromatin binding / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus
Similarity search - Function
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / MDM2 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR
AuthorsYamada, K. / Saito, K. / Nameki, N. / Inoue, M. / Koshiba, S. / Shirouzu, M. / Terada, T. / Yabuki, T. / Aoki, M. / Matsuda, T. ...Yamada, K. / Saito, K. / Nameki, N. / Inoue, M. / Koshiba, S. / Shirouzu, M. / Terada, T. / Yabuki, T. / Aoki, M. / Matsuda, T. / Seki, E. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the SWIB domain of mouse BRG1-associated factor 60a
Authors: Yamada, K. / Saito, K. / Nameki, N. / Inoue, M. / Koshiba, S. / Shirouzu, M. / Terada, T. / Yabuki, T. / Aoki, M. / Matsuda, T. / Seki, E. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. ...Authors: Yamada, K. / Saito, K. / Nameki, N. / Inoue, M. / Koshiba, S. / Shirouzu, M. / Terada, T. / Yabuki, T. / Aoki, M. / Matsuda, T. / Seki, E. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Kigawa, T. / Yokoyama, S.
History
DepositionJul 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily D member 1


Theoretical massNumber of molelcules
Total (without water)10,6341
Polymers10,6341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300target function
RepresentativeModel #1lowest energy

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Components

#1: Protein SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily D member 1 / BRG1-associated factor 60a / BAF60A


Mass: 10634.217 Da / Num. of mol.: 1 / Fragment: SWIB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 0710008A09 / Plasmid: P020826-29 / References: UniProt: Q61466

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 20mM Sodium Phosphate buffer (pH6.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5Johnson, B. A.data analysis
CYANA1Guentart, P.structure solution
KUJIRA0.706Kobayashi, N.data analysis
CYANA1Guentart, P.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 20

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