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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9905 | |||||||||
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Title | RSC substrate-recruitment module | |||||||||
![]() | RSC SRM region | |||||||||
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![]() | chromatin remodeler / SWI/SNF family / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() regulation of sporulation resulting in formation of a cellular spore / chromatin remodeling at centromere / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / regulation of nuclear cell cycle DNA replication / plasmid maintenance / npBAF complex / brahma complex / nBAF complex / DNA translocase activity / nucleosome disassembly ...regulation of sporulation resulting in formation of a cellular spore / chromatin remodeling at centromere / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / regulation of nuclear cell cycle DNA replication / plasmid maintenance / npBAF complex / brahma complex / nBAF complex / DNA translocase activity / nucleosome disassembly / RSC-type complex / UV-damage excision repair / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SWI/SNF complex / nuclear chromosome / sporulation resulting in formation of a cellular spore / rRNA transcription / chromosome, centromeric region / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / cytoskeleton organization / helicase activity / meiotic cell cycle / chromosome segregation / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / double-strand break repair via homologous recombination / lysine-acetylated histone binding / base-excision repair / chromatin DNA binding / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / double-strand break repair / histone binding / DNA helicase / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / 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 / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Ye YP / Wu H | |||||||||
![]() | ![]() Title: Structure of the RSC complex bound to the nucleosome. Authors: Youpi Ye / Hao Wu / Kangjing Chen / Cedric R Clapier / Naveen Verma / Wenhao Zhang / Haiteng Deng / Bradley R Cairns / Ning Gao / Zhucheng Chen / ![]() ![]() Abstract: The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo-electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into ...The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo-electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into the adenosine triphosphatase motor, the actin-related protein module, and the substrate recruitment module (SRM). RSC binds the nucleosome mainly through the motor, with the auxiliary subunit Sfh1 engaging the H2A-H2B acidic patch to enable nucleosome ejection. SRM is organized into three substrate-binding lobes poised to bind their respective nucleosomal epitopes. The relative orientations of the SRM and the motor on the nucleosome explain the directionality of DNA translocation and promoter nucleosome repositioning by RSC. Our findings shed light on RSC assembly and functionality, and they provide a framework to understand the mammalian homologs BAF/PBAF and the Sfh1 ortholog INI1/BAF47, which are frequently mutated in cancers. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 13.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 30.8 KB 30.8 KB | Display Display | ![]() |
Images | ![]() | 50.5 KB | ||
Filedesc metadata | ![]() | 10.2 KB | ||
Others | ![]() ![]() | 166.6 MB 3.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 362 KB | Display | ![]() |
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Full document | ![]() | 361.5 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k15MC ![]() 0777C ![]() 0778C ![]() 6kw3C ![]() 6kw4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RSC SRM region | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: RSC HB lobe
File | emd_9905_additional_1.map | ||||||||||||
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Annotation | RSC HB lobe | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: RSC DB lobe
File | emd_9905_additional_2.map | ||||||||||||
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Annotation | RSC DB lobe | ||||||||||||
Projections & Slices |
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Density Histograms |
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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: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |