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- PDB-1ryu: Solution Structure of the SWI1 ARID -

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Basic information

Entry
Database: PDB / ID: 1ryu
TitleSolution Structure of the SWI1 ARID
ComponentsSWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1
KeywordsDNA BINDING PROTEIN / ARID / SWI1 / structural genomics / protein-DNA interaction
Function / homology
Function and homology information


bBAF complex / npBAF complex / nBAF complex / brahma complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / positive regulation of double-strand break repair ...bBAF complex / npBAF complex / nBAF complex / brahma complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / 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 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) / nuclear receptor binding / positive regulation of cell differentiation / RMTs methylate histone arginines / nervous system development / transcription coactivator activity / chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus
Similarity search - Function
SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / ARID DNA-binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain ...SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / ARID DNA-binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / DNA polymerase; domain 1 / Armadillo-like helical / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model type detailsminimized average
AuthorsKim, S. / Zhang, Z. / Upchurch, S. / Isern, N. / Chen, Y.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure and DNA-binding sites of the SWI1 AT-rich interaction domain (ARID) suggest determinants for sequence-specific DNA recognition.
Authors: Kim, S. / Zhang, Z. / Upchurch, S. / Isern, N. / Chen, Y.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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 F member 1


Theoretical massNumber of molelcules
Total (without water)13,5871
Polymers13,5871
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)8 / 30target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1 / SWI-SNF complex protein p270 / B120


Mass: 13586.547 Da / Num. of mol.: 1 / Fragment: SWI1 ARID (residues 617-736)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O14497

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121(H)CCH-TOCSY
132HN(CA)CB, C(CO)NH, HNCO, HN(CA)CO, H(CCO)NH
1433D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1Approximately 1mM N15/C13 labeled protein in 100mM phosphate buffer, pH 6.0 and 5mM DTT, 100% D2O100% D2O
2Approximately 1mM N15/C13 labeled protein in 100mM phosphate buffer, pH 6.0 and 5mM DTT, 90%H2O/10%D2O90% H2O/10% D2O
3Approximately 1mM N15 labeled protein in 100mM phosphate buffer, pH 6.0 and 5mM DTT, 90%H2O/10%D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM phosphate buffer / pH: 6 / Pressure: 1 atmosphere / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
Felix98,2000Accelrysprocessing
Felix98,2000Accelrysdata analysis
DYANA1.5Gntert, P., Mumenthaler, C. & Wthrich, Kstructure solution
ARIA1.2Jens Linge, Sean O'Donoghue, Michael Nilgesrefinement
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 30 / Conformers submitted total number: 8

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