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- PDB-6l9j: Structure of yeast Snf5 and Swi3 subcomplex -

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Basic information

Entry
Database: PDB / ID: 6l9j
TitleStructure of yeast Snf5 and Swi3 subcomplex
Components
  • SWI/SNF chromatin-remodeling complex subunit SNF5
  • SWI/SNF complex subunit SWI3
KeywordsGENE REGULATION / Complex
Function / homology
Function and homology information


carbon catabolite activation of transcription / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / SWI/SNF complex / nuclear chromosome / double-strand break repair via homologous recombination / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin remodeling / regulation of transcription by RNA polymerase II ...carbon catabolite activation of transcription / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / SWI/SNF complex / nuclear chromosome / double-strand break repair via homologous recombination / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytosol
Similarity search - Function
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 / Myb-like DNA-binding domain ...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 / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
SWI/SNF chromatin-remodeling complex subunit SNF5 / SWI/SNF complex subunit SWI3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.642 Å
AuthorsLong, J. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670758 China
National Natural Science Foundation of China (NSFC)31870750 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Snf5 and Swi3 subcomplex formation is required for SWI/SNF complex function in yeast.
Authors: Zhou, H. / Chen, G. / Dong, C. / Zhao, X. / Shen, Z. / Chen, F. / Liu, B. / Long, J.
History
DepositionNov 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 chromatin-remodeling complex subunit SNF5
B: SWI/SNF complex subunit SWI3
C: SWI/SNF complex subunit SWI3
D: SWI/SNF chromatin-remodeling complex subunit SNF5
E: SWI/SNF complex subunit SWI3
F: SWI/SNF complex subunit SWI3
G: SWI/SNF chromatin-remodeling complex subunit SNF5
H: SWI/SNF complex subunit SWI3
I: SWI/SNF complex subunit SWI3
J: SWI/SNF chromatin-remodeling complex subunit SNF5
K: SWI/SNF complex subunit SWI3
L: SWI/SNF complex subunit SWI3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,93221
Polymers280,10412
Non-polymers8299
Water4,288238
1
A: SWI/SNF chromatin-remodeling complex subunit SNF5
B: SWI/SNF complex subunit SWI3
C: SWI/SNF complex subunit SWI3


Theoretical massNumber of molelcules
Total (without water)70,0263
Polymers70,0263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: SWI/SNF chromatin-remodeling complex subunit SNF5
E: SWI/SNF complex subunit SWI3
F: SWI/SNF complex subunit SWI3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4868
Polymers70,0263
Non-polymers4605
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: SWI/SNF chromatin-remodeling complex subunit SNF5
H: SWI/SNF complex subunit SWI3
I: SWI/SNF complex subunit SWI3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1184
Polymers70,0263
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: SWI/SNF chromatin-remodeling complex subunit SNF5
K: SWI/SNF complex subunit SWI3
L: SWI/SNF complex subunit SWI3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3026
Polymers70,0263
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)205.522, 146.459, 154.329
Angle α, β, γ (deg.)90.000, 131.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
SWI/SNF chromatin-remodeling complex subunit SNF5 / SWI/SNF complex subunit SNF5 / Transcription factor TYE4 / Transcription regulatory protein SNF5


Mass: 26817.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SNF5, SWI10, TYE4, YBR289W, YBR2036 / Production host: Escherichia coli (E. coli) / References: UniProt: P18480
#2: Protein
SWI/SNF complex subunit SWI3 / Transcription factor TYE2 / Transcription regulatory protein SWI3


Mass: 21603.980 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SWI3, TYE2, YJL176C, J0495 / Production host: Escherichia coli (E. coli) / References: UniProt: P32591
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100mM HEPES (pH 7.8), 230mM Li2SO4, 20%-24% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 99168 / % possible obs: 99.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 45.02 Å2 / Rpim(I) all: 0.076 / Net I/σ(I): 8.79
Reflection shellResolution: 2.65→2.7 Å / Num. unique obs: 4909 / Rpim(I) all: 0.365

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: SAD / Resolution: 2.642→48.621 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2795 4875 4.92 %
Rwork0.2285 94217 -
obs0.231 99092 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.85 Å2 / Biso mean: 44.6544 Å2 / Biso min: 17.6 Å2
Refinement stepCycle: final / Resolution: 2.642→48.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13381 0 126 238 13745
Biso mean--53.88 41.28 -
Num. residues----1605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913735
X-RAY DIFFRACTIONf_angle_d0.88918568
X-RAY DIFFRACTIONf_chiral_restr0.0581987
X-RAY DIFFRACTIONf_plane_restr0.0062421
X-RAY DIFFRACTIONf_dihedral_angle_d17.0868289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6425-2.67250.38331280.3118246478
2.6725-2.70390.42741240.3077316698
2.7039-2.73690.35251380.2975318799
2.7369-2.77150.32671450.2944311399
2.7715-2.8080.34641790.2918314699
2.808-2.84650.34351680.2944311699
2.8465-2.88710.37521550.28673187100
2.8871-2.93020.32651580.28543198100
2.9302-2.9760.34171660.27913121100
2.976-3.02480.35371690.28813169100
3.0248-3.07690.37021590.27783213100
3.0769-3.13290.33532000.26783113100
3.1329-3.19310.34541650.26563171100
3.1931-3.25830.3041570.27023169100
3.2583-3.32910.32971510.26523213100
3.3291-3.40650.2891690.24943159100
3.4065-3.49170.32491680.25783159100
3.4917-3.58610.29321710.23673153100
3.5861-3.69160.28522190.2211307798
3.6916-3.81070.2731840.21573163100
3.8107-3.94680.24821600.21173196100
3.9468-4.10480.2431540.19023163100
4.1048-4.29150.22471410.18713220100
4.2915-4.51760.21881460.1823183100
4.5176-4.80040.19691390.1788318599
4.8004-5.17060.23291640.1866315999
5.1706-5.69030.23551950.2027310698
5.6903-6.5120.23171760.21683190100
6.512-8.1980.26561770.2126319599
8.198-48.6210.2841500.2163316396

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