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- PDB-2yus: Solution structure of the SANT domain of human SWI/SNF-related ma... -

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Basic information

Entry
Database: PDB / ID: 2yus
TitleSolution structure of the SANT domain of human SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1
ComponentsSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1
KeywordsTRANSCRIPTION / SWI-SNF complex 155 kDa subunit / BRG1-associated factor 155 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


npBAF complex / prostate gland development / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / XY body / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex ...npBAF complex / prostate gland development / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / XY body / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / 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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of myoblast differentiation / male germ cell nucleus / positive regulation of cell differentiation / animal organ morphogenesis / kinetochore / RMTs methylate histone arginines / nuclear matrix / insulin receptor signaling pathway / nervous system development / histone binding / transcription coactivator activity / chromatin remodeling / chromatin binding / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SMARCC, SWIRM-associated domain / SMARCC, N-terminal / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / SMARCC, C-terminal / SWIRM-associated region 1 / SWIRM domain / SWIRM domain / SWIRM domain profile. ...SMARCC, SWIRM-associated domain / SMARCC, N-terminal / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / SMARCC, C-terminal / SWIRM-associated region 1 / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / BRCT domain superfamily / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SWI/SNF complex subunit SMARCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTochio, N. / Koshiba, S. / Satio, K. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the SANT domain of human SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1
Authors: Tochio, N. / Koshiba, S. / Satio, K. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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

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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 C member 1


Theoretical massNumber of molelcules
Total (without water)8,6221
Polymers8,6221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1 / SWI/SNF complex 155 kDa subunit / BRG1-associated factor 155


Mass: 8622.388 Da / Num. of mol.: 1 / Fragment: UNP residues 610-675, SANT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: SMARCC1 / Plasmid: P050711-15 / References: UniProt: Q92922

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.0mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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