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- PDB-6kag: Crystal structure of the SMARCB1/SMARCC2 subcomplex -

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Basic information

Entry
Database: PDB / ID: 6kag
TitleCrystal structure of the SMARCB1/SMARCC2 subcomplex
Components
  • SWI/SNF complex subunit SMARCC2
  • SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
KeywordsCELL CYCLE / Chromatin remodeling complex / SWI-SNF complex / BAF complex / SMARCB1and SMARCC2 subcomplex / Atypical Teratoid/Rhabdoid tumor
Function / homology
Function and homology information


single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / blastocyst hatching / bBAF complex / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / regulation of G0 to G1 transition ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / blastocyst hatching / bBAF complex / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / regulation of G0 to G1 transition / hepatocyte differentiation / regulation of nucleotide-excision repair / XY body / RSC-type complex / RNA polymerase I preinitiation complex assembly / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / germ cell nucleus / positive regulation of double-strand break repair / 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 / positive regulation of DNA-binding transcription factor activity / p53 binding / RMTs methylate histone arginines / kinetochore / fibrillar center / nuclear matrix / DNA integration / nervous system development / histone binding / transcription coactivator activity / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus
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 ...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 / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / SWI/SNF complex subunit SMARCC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.601 Å
AuthorsChen, G. / Zhou, H. / Giancotti, F.G. / Long, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670758 China
National Natural Science Foundation of China31870750 China
CitationJournal: Cell Discov / Year: 2020
Title: A heterotrimeric SMARCB1-SMARCC2 subcomplex is required for the assembly and tumor suppression function of the BAF chromatin-remodeling complex.
Authors: Chen, G. / Zhou, H. / Liu, B. / Wang, Y. / Zhao, J. / Giancotti, F.G. / Long, J.
History
DepositionJun 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 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

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Assembly

Deposited unit
A: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
B: SWI/SNF complex subunit SMARCC2
C: SWI/SNF complex subunit SMARCC2


Theoretical massNumber of molelcules
Total (without water)69,3013
Polymers69,3013
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, coimmunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-15 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.390, 170.390, 170.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

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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: 24871.975 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 BL21(DE3) (bacteria) / References: UniProt: Q12824
#2: Protein SWI/SNF complex subunit SMARCC2 / BRG1-associated factor 170 / BAF170 / SWI/SNF complex 170 kDa subunit / SWI/SNF-related matrix- ...BRG1-associated factor 170 / BAF170 / SWI/SNF complex 170 kDa subunit / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2


Mass: 22214.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC2, BAF170 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TAQ2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 150 mM CsCl2, 15% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26616 / % possible obs: 100 % / Redundancy: 12.9 % / Rpim(I) all: 0.044 / Net I/σ(I): 17.13
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 2610 / Rpim(I) all: 0.279

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
HKL-2000714data reduction
HKL-2000714data scaling
AutoSol(1.10.1_2155: 000)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.601→49.187 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.43
RfactorNum. reflection% reflection
Rfree0.2402 1348 5.08 %
Rwork0.2066 --
obs0.2083 26525 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.601→49.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 0 115 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092935
X-RAY DIFFRACTIONf_angle_d1.0023983
X-RAY DIFFRACTIONf_dihedral_angle_d19.931748
X-RAY DIFFRACTIONf_chiral_restr0.06433
X-RAY DIFFRACTIONf_plane_restr0.006509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.69410.3481230.28712464X-RAY DIFFRACTION99
2.6941-2.8020.31451240.25952479X-RAY DIFFRACTION100
2.802-2.92950.29921260.23842450X-RAY DIFFRACTION100
2.9295-3.08390.26681320.23752475X-RAY DIFFRACTION100
3.0839-3.27710.28021340.23092491X-RAY DIFFRACTION100
3.2771-3.530.26041450.20992488X-RAY DIFFRACTION100
3.53-3.88510.22661390.18672508X-RAY DIFFRACTION100
3.8851-4.4470.21231330.17062528X-RAY DIFFRACTION100
4.447-5.60150.19751360.17212572X-RAY DIFFRACTION100
5.6015-49.1870.21771560.21852722X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 91.3256 Å / Origin y: 106.2344 Å / Origin z: 39.4776 Å
111213212223313233
T0.3518 Å2-0.0562 Å2-0.0716 Å2-0.2541 Å20.0319 Å2--0.4688 Å2
L0.3174 °2-0.1555 °20.0841 °2-3.0683 °2-0.2706 °2--0.268 °2
S-0.0431 Å °-0.0595 Å °0.0583 Å °0.198 Å °-0.0444 Å °-0.6389 Å °0.025 Å °0.071 Å °0.0816 Å °
Refinement TLS groupSelection details: all

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