+Open data
-Basic information
Entry | Database: PDB / ID: 6k15 | ||||||
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Title | RSC substrate-recruitment module | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / chromatin remodeler / SWI/SNF family | ||||||
Function / homology | Function and homology information regulation of sporulation resulting in formation of a cellular spore / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / plasmid maintenance / DNA translocase activity / nucleosome disassembly / RSC-type complex / UV-damage excision repair / SWI/SNF complex ...regulation of sporulation resulting in formation of a cellular spore / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / plasmid maintenance / DNA translocase activity / nucleosome disassembly / RSC-type complex / UV-damage excision repair / SWI/SNF complex / ATP-dependent chromatin remodeler activity / sister chromatid cohesion / nuclear chromosome / sporulation resulting in formation of a cellular spore / rRNA transcription / chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / meiotic cell cycle / helicase activity / 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 / base-excision repair / lysine-acetylated histone binding / chromatin DNA binding / rRNA processing / double-strand break repair via nonhomologous end joining / double-strand break repair / G2/M transition of mitotic cell cycle / 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 / chromatin / regulation of DNA-templated transcription / 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 | Saccharomyces cerevisiae S288c (yeast) Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Ye, Y.P. / Wu, H. / Chen, K.J. / Verma, N. / Cairns, B. / Gao, N. / Chen, Z.C. | ||||||
Citation | Journal: Science / Year: 2019 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6k15.cif.gz | 591.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k15.ent.gz | 414.8 KB | Display | PDB format |
PDBx/mmJSON format | 6k15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/6k15 ftp://data.pdbj.org/pub/pdb/validation_reports/k1/6k15 | HTTPS FTP |
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-Related structure data
Related structure data | 9905MC 0777C 0778C 6kw3C 6kw4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Chromatin structure-remodeling complex subunit ... , 5 types, 5 molecules FMGXL
#1: Protein | Mass: 49716.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: UniProt: P32832 |
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#3: Protein | Mass: 65289.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q03124 |
#5: Protein | Mass: 48833.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q06168 |
#11: Protein | Mass: 72372.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q02206 |
#12: Protein | Mass: 102443.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q06488 |
-Chromatin structure-remodeling complex protein ... , 5 types, 6 molecules HDIACK
#2: Protein | Mass: 63253.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P43609 #4: Protein | | Mass: 54222.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P25632 #6: Protein | | Mass: 57871.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q07979 #9: Protein | | Mass: 101448.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P38781 #10: Protein | | Mass: 101833.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q06639 |
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-Protein , 2 types, 2 molecules JE
#7: Protein | Mass: 156982.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P32597, DNA helicase |
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#8: Protein | Mass: 9192.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q9URQ5 |
-Non-polymers , 1 types, 1 molecules
#13: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RSC / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DARK FIELD |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280000 / Symmetry type: POINT |