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- PDB-7c4j: Cryo-EM structure of the yeast Swi/Snf complex in a nucleosome fr... -
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Basic information
Entry | Database: PDB / ID: 7c4j | |||||||||
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Title | Cryo-EM structure of the yeast Swi/Snf complex in a nucleosome free state | |||||||||
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![]() | DNA BINDING PROTEIN / SWI/SNF remodeling / Swi-Snf complex / nucleosome | |||||||||
Function / homology | ![]() carbon catabolite activation of transcription from RNA polymerase II promoter / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation ...carbon catabolite activation of transcription from RNA polymerase II promoter / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation / rDNA binding / HDACs deacetylate histones / nucleosome disassembly / DNA strand invasion / RSC-type complex / ATP-dependent chromatin remodeler activity / SUMOylation of chromatin organization proteins / SWI/SNF complex / nuclear chromosome / NuA4 histone acetyltransferase complex / positive regulation of transcription by RNA polymerase I / anatomical structure morphogenesis / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / helicase activity / maturation of LSU-rRNA / chromosome segregation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription coregulator activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via homologous recombination / lysine-acetylated histone binding / chromatin DNA binding / DNA-templated DNA replication / double-strand break repair / chromatin organization / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / 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 / DNA binding / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
![]() | Wang, C.C. / Guo, Z.Y. / Zhan, X.C. / Zhang, X.F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the yeast Swi/Snf complex in a nucleosome free state. Authors: Chengcheng Wang / Zhouyan Guo / Xiechao Zhan / Fenghua Yang / Mingxuan Wu / Xiaofeng Zhang / ![]() Abstract: SWI/SNF remodelers play a key role in regulating chromatin architecture and gene expression. Here, we report the cryo-EM structure of the Saccharomyces cerevisiae Swi/Snf complex in a nucleosome-free ...SWI/SNF remodelers play a key role in regulating chromatin architecture and gene expression. Here, we report the cryo-EM structure of the Saccharomyces cerevisiae Swi/Snf complex in a nucleosome-free state. The structure consists of a stable triangular base module and a flexible Arp module. The conserved subunits Swi1 and Swi3 form the backbone of the complex and closely interact with other components. Snf6, which is specific for yeast Swi/Snf complex, stabilizes the binding of the ATPase-containing subunit Snf2 to the base module. Comparison of the yeast Swi/Snf and RSC complexes reveals conserved structural features that govern the assembly and function of these two subfamilies of chromatin remodelers. Our findings complement those from recent structures of the yeast and human chromatin remodelers and provide further insights into the assembly and function of the SWI/SNF remodelers. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 766.9 KB | Display | ![]() |
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PDB format | ![]() | 571 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 93.7 KB | Display | |
Data in CIF | ![]() | 145.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30285MC 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
-Transcription regulatory protein ... , 3 types, 3 molecules ACH
#1: Protein | Mass: 63947.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 37652.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 194315.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P22082, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
-Protein , 6 types, 7 molecules BDEGJKL
#2: Protein | Mass: 93034.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 70366.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | | Mass: 7600.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | | Mass: 17817.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | | Mass: 53863.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | | Mass: 53131.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-SWI/SNF chromatin-remodeling complex subunit ... , 2 types, 2 molecules FI
#5: Protein | Mass: 102642.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#7: Protein | Mass: 148065.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Details
Sequence details | Authors state that the residues except Ala were basically generated from our EM map and seem like ...Authors state that the residues except Ala were basically generated from our EM map and seem like those side-chains for the chain G (unknown molecule). |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: the yeast Swi/Snf complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 1.14 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
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: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386469 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 2.89 Å | ||||||||||||||||||||||||
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