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- PDB-6lzp: The solution structure of N-terminal elongated hSNF5 RPT1 domain -

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Basic information

Entry
Database: PDB / ID: 6lzp
TitleThe solution structure of N-terminal elongated hSNF5 RPT1 domain
ComponentsSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
KeywordsSTRUCTURAL PROTEIN / Chromatin remodeling complex SWI-SNF COMPLEX / TUMOR SUPPRESSOR / TRANSCRIPTION / Structural Genomics / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / blastocyst hatching / bBAF complex / npBAF complex / brahma complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / regulation of G0 to G1 transition ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / blastocyst hatching / bBAF complex / npBAF complex / brahma complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / regulation of G0 to G1 transition / Tat protein binding / nucleosome disassembly / regulation of nucleotide-excision repair / hepatocyte differentiation / XY body / RSC-type complex / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / germ cell nucleus / positive regulation of T cell differentiation / nuclear chromosome / 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 / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / positive regulation of cell differentiation / kinetochore / fibrillar center / RMTs methylate histone arginines / positive regulation of DNA-binding transcription factor activity / nuclear matrix / DNA integration / p53 binding / nervous system development / transcription coactivator activity / chromatin remodeling / cell cycle / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin / nucleolus / regulation of transcription by RNA polymerase II / 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 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLee, W. / Han, J. / Kim, I. / Suh, J.Y.
Funding support Korea, Republic Of, United States, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017R1A2B2008483 Korea, Republic Of
Rural Development AdministrationPJ011112 United States
CitationJournal: Int J Mol Sci / Year: 2020
Title: A Coil-to-Helix Transition Serves as a Binding Motif for hSNF5 and BAF155 Interaction.
Authors: Han, J. / Kim, I. / Park, J.H. / Yun, J.H. / Joo, K. / Kim, T. / Park, G.Y. / Ryu, K.S. / Ko, Y.J. / Mizutani, K. / Park, S.Y. / Seong, R.H. / Lee, J. / Suh, J.Y. / Lee, W.
History
DepositionFeb 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _pdbx_audit_support.country

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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)10,0761
Polymers10,0761
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7650 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100020
RepresentativeModel #1lowest energy

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Components

#1: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Mass: 10076.294 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCB1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0G2JRV3, UniProt: Q12824*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D CBCA(CO)NH
131isotropic23D HN(CA)CB
141isotropic23D HNCO
151isotropic23D HNHA
171isotropic23D H(CCO)NH
161isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution / Contents: 0.5 mM 15N hSNF5(171-258), 90% H2O/10% D2O / Label: 13C_15N_hSNF5(171-258) / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: hSNF5(171-258) / Isotopic labeling: 15N
Sample conditionsIonic strength: 150 mM / Label: solution / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
X-PLOR NIH2.52Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 / Conformers calculated total number: 1000 / Conformers submitted total number: 20

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