+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0779 | |||||||||
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Title | The ClassC RSC-Nucleosome Complex | |||||||||
Map data | The ClassC RSC-Nucleosome Complex | |||||||||
Sample |
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Keywords | chromatin remodeler / SWI/SNF family / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information regulation of sporulation resulting in formation of a cellular spore / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / plasmid maintenance / Platelet degranulation / DNA translocase activity / RSC-type complex ...regulation of sporulation resulting in formation of a cellular spore / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / plasmid maintenance / Platelet degranulation / DNA translocase activity / RSC-type complex / UV-damage excision repair / SWI/SNF complex / nucleosome disassembly / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / nuclear chromosome / sporulation resulting in formation of a cellular spore / NuA4 histone acetyltransferase complex / rRNA transcription / nucleosome binding / chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / meiotic cell cycle / DNA-templated transcription initiation / chromosome segregation / helicase activity / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / double-strand break repair via homologous recombination / base-excision repair / chromatin DNA binding / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / G2/M transition of mitotic cell cycle / nucleosome / double-strand break repair / nucleosome assembly / chromatin organization / histone binding / DNA helicase / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Xenopus laevis (African clawed frog) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.13 Å | |||||||||
Authors | Ye YP / Wu H | |||||||||
Citation | Journal: To Be Published Title: Structure of the RSC complex bound to the nucleosome Authors: Ye YP / Wu H / Chen KJ / Verma N / Cairns B / Gao N / Chen ZC | |||||||||
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_0779.map.gz | 20.9 MB | EMDB map data format | |
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Header (meta data) | emd-0779-v30.xml emd-0779.xml | 37.4 KB 37.4 KB | Display Display | EMDB header |
Images | emd_0779.png | 63.8 KB | ||
Filedesc metadata | emd-0779.cif.gz | 12.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0779 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0779 | HTTPS FTP |
-Validation report
Summary document | emd_0779_validation.pdf.gz | 415.5 KB | Display | EMDB validaton report |
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Full document | emd_0779_full_validation.pdf.gz | 415.1 KB | Display | |
Data in XML | emd_0779_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_0779_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0779 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0779 | HTTPS FTP |
-Related structure data
Related structure data | 6kw5MC M: atomic model generated by this map C: citing same article (ref.) |
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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_0779.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The ClassC RSC-Nucleosome Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.14 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 : RSC
+Supramolecule #1: RSC
+Macromolecule #1: Chromatin structure-remodeling complex subunit RSC7
+Macromolecule #2: Chromatin structure-remodeling complex protein RSC8
+Macromolecule #3: Chromatin structure-remodeling complex subunit RSC9
+Macromolecule #4: Chromatin structure-remodeling complex protein RSC6
+Macromolecule #5: Chromatin structure-remodeling complex subunit SFH1
+Macromolecule #6: Chromatin structure-remodeling complex protein RSC58
+Macromolecule #7: Nuclear protein STH1/NPS1
+Macromolecule #8: High temperature lethal protein 1
+Macromolecule #9: Chromatin structure-remodeling complex protein RSC30
+Macromolecule #10: Chromatin structure-remodeling complex protein RSC3
+Macromolecule #11: Chromatin structure-remodeling complex subunit RSC4
+Macromolecule #12: Chromatin structure-remodeling complex subunit RSC2
+Macromolecule #13: Histone H4
+Macromolecule #14: Actin-related protein 7
+Macromolecule #15: Regulator of Ty1 transposition protein 102
+Macromolecule #16: Histone H3.2
+Macromolecule #17: Histone H2A
+Macromolecule #18: Histone H4
+Macromolecule #19: Actin-like protein ARP9
+Macromolecule #20: DNA 167
+Macromolecule #21: DNA 167
+Macromolecule #22: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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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 K2 QUANTUM (4k x 4k) / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 10.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24146 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |