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- PDB-6kz7: The crystal structure of BAF155 SWIRM domain and N-terminal elong... -

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Basic information

Entry
Database: PDB / ID: 6kz7
TitleThe crystal structure of BAF155 SWIRM domain and N-terminal elongated hSNF5 RPT1 domain complex: Chromatin remodeling complex
Components
  • SWI/SNF complex subunit SMARCC1
  • SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
KeywordsTRANSCRIPTION / SWI-SNF COMPLEX / TUMOR SUPPRESSOR
Function / homology
Function and homology information


single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / blastocyst hatching / bBAF complex / npBAF complex / prostate gland development / brahma complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / blastocyst hatching / bBAF complex / npBAF complex / prostate gland development / brahma complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / XY body / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / hepatocyte differentiation / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / 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 / negative regulation of cell differentiation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / male germ cell nucleus / positive regulation of cell differentiation / animal organ morphogenesis / kinetochore / fibrillar center / RMTs methylate histone arginines / nuclear matrix / DNA integration / positive regulation of DNA-binding transcription factor activity / p53 binding / insulin receptor signaling pathway / nervous system development / histone binding / transcription coactivator activity / chromatin remodeling / cell cycle / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin binding / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / 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. / : / SWI/SNF Subunit INI1, DNA binding domain / Chromatin-remodeling complex component Sfh1/SNF5 / SMARCC, C-terminal / SWIRM-associated region 1 ...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. / : / SWI/SNF Subunit INI1, DNA binding domain / Chromatin-remodeling complex component Sfh1/SNF5 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / 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 / BRCT domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / SWI/SNF complex subunit SMARCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLee, W. / Han, J. / Kim, I. / Park, J.H. / Joo, K. / Lee, J. / Suh, J.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017R1A2B2008483 Korea, Republic Of
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
DepositionSep 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: SWI/SNF complex subunit SMARCC1
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
C: SWI/SNF complex subunit SMARCC1
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)41,0594
Polymers41,0594
Non-polymers00
Water4,017223
1
A: SWI/SNF complex subunit SMARCC1
B: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)20,5292
Polymers20,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-7 kcal/mol
Surface area9700 Å2
MethodPISA
2
C: SWI/SNF complex subunit SMARCC1
D: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)20,5292
Polymers20,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-7 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.232, 77.232, 207.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein SWI/SNF complex subunit SMARCC1 / / BRG1-associated factor 155 / BAF155 / SWI/SNF complex 155 kDa subunit / SWI/SNF-related matrix- ...BRG1-associated factor 155 / BAF155 / SWI/SNF complex 155 kDa subunit / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1


Mass: 11195.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC1, BAF155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92922
#2: 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: 9333.520 Da / Num. of mol.: 2
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) / References: UniProt: Q12824
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 288 K / Method: microbatch
Details: TACSIMATE, HEPES, PEC3350, MICROBATCH, TEMPERATURE 288K

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→28.1 Å / Num. obs: 20987 / % possible obs: 99.87 % / Redundancy: 5.43 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.16
Reflection shellResolution: 2.28→2.343 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3.01 / Num. unique obs: 2069 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→28.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2003 1818 8.66 %
Rwork0.1661 --
obs0.1695 20987 99.87 %
Refinement stepCycle: LAST / Resolution: 2.28→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 0 223 3099

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