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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 / regulation of nuclear cell cycle DNA replication / plasmid maintenance / DNA translocase activity / RSC-type complex / UV-damage excision repair / sister chromatid cohesion / SWI/SNF complex / nucleosome disassembly ...regulation of sporulation resulting in formation of a cellular spore / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / plasmid maintenance / DNA translocase activity / RSC-type complex / UV-damage excision repair / sister chromatid cohesion / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / nuclear chromosome / sporulation resulting in formation of a cellular spore / rRNA transcription / chromosome, centromeric region / nucleosome binding / ATP-dependent activity, acting on DNA / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / cytoskeleton organization / lysine-acetylated histone binding / helicase activity / chromosome segregation / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / base-excision repair / chromatin DNA binding / G2/M transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / double-strand break repair / histone binding / DNA helicase / sequence-specific DNA binding / 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 transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / structural molecule activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / 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 |
-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
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Annotation | RSC SRM region | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |