+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31137 | |||||||||
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Title | The structure of SWI/SNF-nucleosome complex | |||||||||
Map data | The structure of SWI/SNF-nucleosome complex | |||||||||
Sample |
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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 / DNA strand invasion ...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 / DNA strand invasion / rDNA binding / HDACs deacetylate histones / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / SUMOylation of chromatin organization proteins / ATP-dependent chromatin remodeler activity / nuclear chromosome / NuA4 histone acetyltransferase complex / positive regulation of transcription by RNA polymerase I / ATP-dependent activity, acting on DNA / maturation of LSU-rRNA / nucleosomal DNA binding / cellular response to amino acid starvation / transcription initiation-coupled chromatin remodeling / histone reader activity / chromosome segregation / nucleotide-excision repair / helicase activity / transcription elongation by RNA polymerase II / lysine-acetylated histone binding / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / DNA-templated DNA replication / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / chromatin organization / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / structural molecule activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.9 Å | |||||||||
Authors | Chen ZC / Chen KJ / He ZY / Ye YP | |||||||||
Citation | Journal: Cell Discov / Year: 2021 Title: Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity. Authors: Zhenyu He / Kangjing Chen / Youpi Ye / Zhucheng Chen / | |||||||||
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_31137.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-31137-v30.xml emd-31137.xml | 36.9 KB 36.9 KB | Display Display | EMDB header |
Images | emd_31137.png | 82.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31137 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31137 | HTTPS FTP |
-Validation report
Summary document | emd_31137_validation.pdf.gz | 311 KB | Display | EMDB validaton report |
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Full document | emd_31137_full_validation.pdf.gz | 310.6 KB | Display | |
Data in XML | emd_31137_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_31137_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31137 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31137 | HTTPS FTP |
-Related structure data
Related structure data | 7egpMC 7eg6C 7egmC 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_31137.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The structure of SWI/SNF-nucleosome complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.1484 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 structure of SWI/SNF chromatin remodeler complex
+Supramolecule #1: The structure of SWI/SNF chromatin remodeler complex
+Supramolecule #2: SWI/SNF
+Supramolecule #3: Histone
+Supramolecule #4: DNA
+Macromolecule #1: SWI/SNF chromatin-remodeling complex subunit SWI1
+Macromolecule #2: SWI/SNF chromatin-remodeling complex subunit SNF5
+Macromolecule #3: SWI/SNF complex subunit SWI3
+Macromolecule #4: Transcription regulatory protein SNF12
+Macromolecule #5: Transcription regulatory protein SNF6
+Macromolecule #6: SWI/SNF global transcription activator complex subunit SWP82
+Macromolecule #7: Transcription regulatory protein SNF2
+Macromolecule #8: Regulator of Ty1 transposition protein 102
+Macromolecule #9: Actin-related protein 7
+Macromolecule #10: Actin-like protein ARP9
+Macromolecule #11: Histone H3.2
+Macromolecule #12: Histone H4
+Macromolecule #13: Histone H2A
+Macromolecule #14: Histone H2B 1.1
+Macromolecule #15: DNA (239-MER)
+Macromolecule #16: DNA (239-MER)
+Macromolecule #17: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #18: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #19: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
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: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229461 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: OTHER |