+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20934 | ||||||||||||
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Title | SWI/SNF nucleosome complex with ADP-BeFx | ||||||||||||
Map data | SWI/SNF nucleosome complex assembled in the presence of ADP-BeFx | ||||||||||||
Sample |
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Keywords | 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 | Saccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.96 Å | ||||||||||||
Authors | He Y / Han Y | ||||||||||||
Funding support | United States, 3 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20934.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-20934-v30.xml emd-20934.xml | 38.8 KB 38.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20934_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_20934.png | 76.2 KB | ||
Filedesc metadata | emd-20934.cif.gz | 11.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20934 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20934 | HTTPS FTP |
-Validation report
Summary document | emd_20934_validation.pdf.gz | 388.5 KB | Display | EMDB validaton report |
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Full document | emd_20934_full_validation.pdf.gz | 388 KB | Display | |
Data in XML | emd_20934_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | emd_20934_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20934 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20934 | HTTPS FTP |
-Related structure data
Related structure data | 6uxwMC 6uxvC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20934.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SWI/SNF nucleosome complex assembled in the presence of ADP-BeFx | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : SWI/SNF nucleosome complex with ADP-BeFx
+Supramolecule #1: SWI/SNF nucleosome complex with ADP-BeFx
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: Actin-related protein 7
+Macromolecule #8: Actin-like protein ARP9
+Macromolecule #9: Regulator of Ty1 transposition protein 102
+Macromolecule #10: Transcription regulatory protein SNF2
+Macromolecule #11: SWI/SNF chromatin-remodeling complex subunit SWI1
+Macromolecule #12: SWI/SNF chromatin-remodeling complex subunit SNF5
+Macromolecule #13: SWI/SNF complex subunit SWI3
+Macromolecule #14: Transcription regulatory protein SNF12
+Macromolecule #15: Transcription regulatory protein SNF6
+Macromolecule #16: Unknown protein
+Macromolecule #17: SWI/SNF global transcription activator complex subunit SWP82
+Macromolecule #5: 601 sequence bottom strand
+Macromolecule #6: 601 sequence top strand
+Macromolecule #18: PHOSPHATE ION
+Macromolecule #19: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #20: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #21: MAGNESIUM ION
+Macromolecule #22: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | 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 |
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Grid | Support film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL 3200FS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 76.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |