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- PDB-5l7b: Solution structure of the human SNF5/INI1 domain -

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Basic information

Entry
Database: PDB / ID: 5l7b
TitleSolution structure of the human SNF5/INI1 domain
ComponentsSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
KeywordsDNA BINDING PROTEIN / SNF5/INI1 NMR structure
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 / SWI/SNF complex / nucleosome disassembly / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / positive regulation of stem cell population maintenance / nuclear chromosome / 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 / kinetochore / fibrillar center / 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 / torsion angle dynamics
AuthorsAllen, M.D. / Zinzalla, G. / Bycroft, M.
CitationJournal: FEBS J. / Year: 2018
Title: The structure of INI1/hSNF5 RPT1 and its interactions with the c-MYC:MAX heterodimer provide insights into the interplay between MYC and the SWI/SNF chromatin remodeling complex.
Authors: Sammak, S. / Allen, M.D. / Hamdani, N. / Bycroft, M. / Zinzalla, G.
History
DepositionJun 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Nov 6, 2019Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.5May 15, 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)8,8221
Polymers8,8221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5790 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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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


Mass: 8821.944 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 (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / 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
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D DQF-COSY
142isotropic23D HN(CA)CB
1102isotropic23D CBCA(CO)NH
192isotropic23D HNCO
182isotropic23D HN(CA)CO
172isotropic23D HNHB
162isotropic23D HBHA(CO)NH
152isotropic22D 1H-15N HSQC
1112isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetails (eV)LabelSolvent system
solution120 mM potassium phosphate, 100 mM sodium chloride, 5 mM [U-100% 2H] beta-mercaptoethanol, 90% H2O/10% D2OSamples were typically 1.5mM in 20mM potassium phosphate containing 100mM NaCl1H90% H2O/10% D2O
solution220 mM potassium phosphate, 100 mM sodium chloride, 5 mM [U-100% 2H] beta-mercaptoethanol, 90% H2O/10% D2O15N/13C90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMpotassium phosphatenone1
100 mMsodium chloridenone1
5 mMbeta-mercaptoethanol[U-100% 2H]1
20 mMpotassium phosphatenone2
100 mMsodium chloridenone2
5 mMbeta-mercaptoethanol[U-100% 2H]2
Sample conditionsDetails: 1.5mM protein in the standard buffer / Ionic strength: 120 mM / Label: standard conditions / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ANSIGKraulischemical shift assignment
ANSIGKraulispeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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