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Yorodumi- EMDB-30285: Cryo-EM structure of the yeast Swi/Snf complex in a nucleosome fr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30285 | |||||||||
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Title | Cryo-EM structure of the yeast Swi/Snf complex in a nucleosome free state | |||||||||
Map data | The 2.9 angstrom EM map of the yeast Swi/Snf complex in a nucleosome free state | |||||||||
Sample |
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Keywords | SWI/SNF remodeling / Swi-Snf complex / nucleosome / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information carbon catabolite activation of transcription from RNA polymerase II promoter / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation / HDACs deacetylate histones ...carbon catabolite activation of transcription from RNA polymerase II promoter / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation / HDACs deacetylate histones / DNA strand invasion / rDNA binding / DNA translocase activity / RSC-type complex / SUMOylation of chromatin organization proteins / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / nuclear chromosome / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / maturation of LSU-rRNA / cellular response to amino acid starvation / chromosome segregation / helicase activity / nucleotide-excision repair / transcription elongation by RNA polymerase II / lysine-acetylated histone binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via homologous recombination / chromatin DNA binding / DNA-templated DNA replication / structural constituent of chromatin / double-strand break repair / chromatin organization / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
Authors | Wang CC / Guo ZY | |||||||||
Funding support | China, 2 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structure of the yeast Swi/Snf complex in a nucleosome free state. Authors: Chengcheng Wang / Zhouyan Guo / Xiechao Zhan / Fenghua Yang / Mingxuan Wu / Xiaofeng Zhang / Abstract: SWI/SNF remodelers play a key role in regulating chromatin architecture and gene expression. Here, we report the cryo-EM structure of the Saccharomyces cerevisiae Swi/Snf complex in a nucleosome-free ...SWI/SNF remodelers play a key role in regulating chromatin architecture and gene expression. Here, we report the cryo-EM structure of the Saccharomyces cerevisiae Swi/Snf complex in a nucleosome-free state. The structure consists of a stable triangular base module and a flexible Arp module. The conserved subunits Swi1 and Swi3 form the backbone of the complex and closely interact with other components. Snf6, which is specific for yeast Swi/Snf complex, stabilizes the binding of the ATPase-containing subunit Snf2 to the base module. Comparison of the yeast Swi/Snf and RSC complexes reveals conserved structural features that govern the assembly and function of these two subfamilies of chromatin remodelers. Our findings complement those from recent structures of the yeast and human chromatin remodelers and provide further insights into the assembly and function of the SWI/SNF remodelers. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30285.map.gz | 117 MB | EMDB map data format | |
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Header (meta data) | emd-30285-v30.xml emd-30285.xml | 25.6 KB 25.6 KB | Display Display | EMDB header |
Images | emd_30285.png | 155.2 KB | ||
Filedesc metadata | emd-30285.cif.gz | 9.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30285 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30285 | HTTPS FTP |
-Validation report
Summary document | emd_30285_validation.pdf.gz | 561.7 KB | Display | EMDB validaton report |
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Full document | emd_30285_full_validation.pdf.gz | 561.3 KB | Display | |
Data in XML | emd_30285_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_30285_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30285 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30285 | HTTPS FTP |
-Related structure data
Related structure data | 7c4jMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30285.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The 2.9 angstrom EM map of the yeast Swi/Snf complex in a nucleosome free state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : the yeast Swi/Snf complex
+Supramolecule #1: the yeast Swi/Snf complex
+Macromolecule #1: Transcription regulatory protein SNF12
+Macromolecule #2: SWI/SNF complex subunit SWI3
+Macromolecule #3: Transcription regulatory protein SNF6
+Macromolecule #4: SWI/SNF global transcription activator complex subunit SWP82
+Macromolecule #5: SWI/SNF chromatin-remodeling complex subunit SNF5
+Macromolecule #6: Transcription regulatory protein SNF2
+Macromolecule #7: SWI/SNF chromatin-remodeling complex subunit SWI1
+Macromolecule #8: Unkown
+Macromolecule #9: Regulator of Ty1 transposition protein 102
+Macromolecule #10: Actin-related protein 7
+Macromolecule #11: Actin-like protein ARP9
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 386469 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |