+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31106 | |||||||||
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Title | Snf5 Finger Helix bound to the nucleosome | |||||||||
Map data | The structure of Snf5 Finger Helix bound to the nucleosome | |||||||||
Sample |
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Keywords | Chromatin remodeler complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of invasive growth in response to glucose limitation / SWI/SNF complex / nuclear chromosome / double-strand break repair via homologous recombination / structural constituent of chromatin / nucleosome / nucleosome assembly / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin remodeling ...carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of invasive growth in response to glucose limitation / SWI/SNF complex / nuclear chromosome / double-strand break repair via homologous recombination / structural constituent of chromatin / nucleosome / nucleosome assembly / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin remodeling / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Chen ZC / Chen KJ | |||||||||
Citation | Journal: Cell Discov / Year: 2021 Title: Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity. Authors: Zhenyu He / Kangjing Chen / Youpi Ye / Zhucheng Chen / | |||||||||
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_31106.map.gz | 8.5 MB | EMDB map data format | |
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Header (meta data) | emd-31106-v30.xml emd-31106.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
Images | emd_31106.png | 89.8 KB | ||
Filedesc metadata | emd-31106.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31106 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31106 | HTTPS FTP |
-Validation report
Summary document | emd_31106_validation.pdf.gz | 325.6 KB | Display | EMDB validaton report |
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Full document | emd_31106_full_validation.pdf.gz | 325.2 KB | Display | |
Data in XML | emd_31106_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_31106_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31106 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31106 | HTTPS FTP |
-Related structure data
Related structure data | 7eg6MC 7egmC 7egpC M: atomic model generated by this map C: citing same article (ref.) |
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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_31106.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The structure of Snf5 Finger Helix bound to the nucleosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0742 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 : Chromatin remodeler complex SWI/SNF, Snf5 Finger Helix bound to t...
+Supramolecule #1: Chromatin remodeler complex SWI/SNF, Snf5 Finger Helix bound to t...
+Supramolecule #2: Snf5 Finger Helix
+Supramolecule #3: Histone
+Supramolecule #4: DNA
+Macromolecule #1: SWI/SNF chromatin-remodeling complex subunit SNF5
+Macromolecule #2: Histone H3.2
+Macromolecule #3: Histone H4
+Macromolecule #4: Histone H2A type 1
+Macromolecule #5: Histone H2B 1.1
+Macromolecule #6: DNA (235-MER)
+Macromolecule #7: DNA (235-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 525389 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: OTHER |