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Open data
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Basic information
Entry | Database: PDB / ID: 6kw3 | ||||||
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Title | The ClassA RSC-Nucleosome Complex | ||||||
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![]() | DNA BINDING PROTEIN/DNA / chromatin remodeler / SWI/SNF family / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() 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 / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / regulation of nuclear cell cycle DNA replication / plasmid maintenance / Platelet degranulation / npBAF 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 / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / regulation of nuclear cell cycle DNA replication / plasmid maintenance / Platelet degranulation / 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 / NuA4 histone acetyltransferase complex / rRNA transcription / chromosome, centromeric region / anatomical structure morphogenesis / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / cytoskeleton organization / helicase activity / meiotic cell cycle / DNA-templated transcription initiation / 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 / 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 / transcription coactivator activity / 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 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.13 Å | ||||||
![]() | Ye, Y.P. / Wu, H. / Chen, K.J. / Verma, N. / Cairns, B. / Gao, N. / Chen, Z.C. | ||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 930 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1006.1 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 116.3 KB | Display | |
Data in CIF | ![]() | 186 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0777MC ![]() 0778C ![]() 9905C ![]() 6k15C ![]() 6kw4C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 9 types, 15 molecules BRNQOSWJYfhETPg
#1: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 15421.101 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Protein | Mass: 156982.406 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32597, DNA helicase #7: Protein | | Mass: 53863.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12406 #8: Protein | | Mass: 17817.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P53330 #15: Protein | | Mass: 9192.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q9URQ5 #20: Protein | Mass: 13925.202 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #21: Protein | | Mass: 53131.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q05123 |
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-DNA chain , 2 types, 2 molecules UV
#4: DNA chain | Mass: 51421.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#5: DNA chain | Mass: 51683.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Chromatin structure-remodeling complex subunit ... , 5 types, 5 molecules FMGXL
#9: Protein | Mass: 49716.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32832 |
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#11: Protein | Mass: 65289.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q03124 |
#13: Protein | Mass: 48833.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06168 |
#18: Protein | Mass: 72372.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q02206 |
#19: Protein | Mass: 102443.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06488 |
-Chromatin structure-remodeling complex protein ... , 5 types, 6 molecules HDIACK
#10: Protein | Mass: 63253.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P43609 #12: Protein | | Mass: 54222.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P25632 #14: Protein | | Mass: 57871.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q07979 #16: Protein | | Mass: 101448.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38781 #17: Protein | | Mass: 101833.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06639 |
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-Non-polymers , 1 types, 1 molecules ![](data/chem/img/ZN.gif)
#22: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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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 |
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Sample preparation
Component | Name: RSC / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: DARK FIELD |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 7.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45077 / Symmetry type: POINT |