+Open data
-Basic information
Entry | Database: PDB / ID: 6uxw | ||||||||||||
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Title | SWI/SNF nucleosome complex with ADP-BeFx | ||||||||||||
Components |
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Keywords | TRANSCRIPTION/DNA / SWI/SNF / chromatin remodeler / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||||||||
Function / homology | Function and homology information 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 invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation / rDNA binding ...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 invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation / rDNA binding / HDACs deacetylate histones / DNA translocase activity / DNA strand invasion / RSC-type complex / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / nuclear chromosome / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / lysine-acetylated histone binding / maturation of LSU-rRNA / cellular response to amino acid starvation / helicase activity / chromosome segregation / nucleotide-excision repair / transcription elongation by RNA polymerase II / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via homologous recombination / DNA-templated DNA replication / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / chromatin organization / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / hydrolase activity / protein heterodimerization activity / 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 / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288C (yeast) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.96 Å | ||||||||||||
Authors | He, Y. / Han, Y. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nature / Year: 2020 Title: Cryo-EM structure of SWI/SNF complex bound to a nucleosome. Authors: Yan Han / Alexis A Reyes / Sara Malik / Yuan He / Abstract: The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel ...The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair. It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers, creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation. | ||||||||||||
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 | 6uxw.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6uxw.ent.gz | 979.7 KB | Display | PDB format |
PDBx/mmJSON format | 6uxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uxw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6uxw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6uxw_validation.xml.gz | 131.5 KB | Display | |
Data in CIF | 6uxw_validation.cif.gz | 204.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/6uxw ftp://data.pdbj.org/pub/pdb/validation_reports/ux/6uxw | HTTPS FTP |
-Related structure data
Related structure data | 20934MC 6uxvC 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
-Protein , 10 types, 21 molecules RVSWTXUYPQZDEFGJKLNOM
#1: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897 #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RESIDUES 597-653 AND 765-780 OF CHAIN F, AND RESIDUES 609-655 AND 763-779 OF CHAIN G ARE NOT CONFIDENTLY ASSIGNED Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 #7: Protein | | Mass: 53863.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q12406 #8: Protein | | Mass: 53131.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q05123 #9: Protein | | Mass: 17817.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P53330 #13: Protein | Mass: 93034.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P32591 #16: Protein | Mass: 5720.042 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c #17: Protein | | Mass: 7081.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
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-601 sequence ... , 2 types, 2 molecules ab
#5: DNA chain | Mass: 56943.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 61785.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Transcription regulatory protein ... , 3 types, 3 molecules AHI
#10: Protein | Mass: 194315.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P22082, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#14: Protein | Mass: 63947.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P53628 |
#15: Protein | Mass: 19565.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (natural) Saccharomyces cerevisiae S288C (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P18888 |
-SWI/SNF chromatin-remodeling complex subunit ... , 2 types, 2 molecules BC
#11: Protein | Mass: 148065.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P09547 |
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#12: Protein | Mass: 102642.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P18480 |
-Non-polymers , 5 types, 101 molecules
#18: Chemical | ChemComp-PO4 / #19: Chemical | ChemComp-ADP / | #20: Chemical | ChemComp-BEF / | #21: Chemical | ChemComp-MG / | #22: Water | ChemComp-HOH / | |
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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: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SWI/SNF nucleosome complex with ADP-BeFx / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Buffer solution | pH: 7.9 Details: 10 mM HEPES, pH 7.9, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol, 0.05% NP-40 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Electron dose: 76.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: CTF amplitude correction was performed following 3D auto refinement in relion. Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 8.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35214 / Symmetry type: POINT | ||||||||||||||||||||||||||||
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