+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4396 | ||||||||||||||||||
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Title | Chromatin remodeller-nucleosome complex at 4.5 A resolution. | ||||||||||||||||||
Map data | Chromatin remodeller-nucleosome complex at 4.5 A resolution. | ||||||||||||||||||
Sample |
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Keywords | Chromatin / Remodeller / ATPase / Histone / NUCLEAR PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information RNA polymerase I upstream activating factor complex / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / cupric reductase (NADH) activity / global genome nucleotide-excision repair / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / R2TP complex ...RNA polymerase I upstream activating factor complex / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / cupric reductase (NADH) activity / global genome nucleotide-excision repair / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / R2TP complex / HDACs deacetylate histones / Swr1 complex / protein targeting to vacuole / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Ino80 complex / replication fork protection complex / RMTs methylate histone arginines / Oxidative Stress Induced Senescence / postreplication repair / prenyltransferase activity / box C/D snoRNP assembly / recombinational repair / ATP-dependent chromatin remodeler activity / isoprenoid biosynthetic process / 3'-5' DNA helicase activity / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / nucleosome binding / intracellular copper ion homeostasis / Ub-specific processing proteases / CENP-A containing nucleosome / nucleosomal DNA binding / DNA helicase activity / aerobic respiration / nuclear periphery / helicase activity / heterochromatin formation / structural constituent of chromatin / rRNA processing / nucleosome / chromatin organization / histone binding / 5'-3' DNA helicase activity / DNA helicase / molecular adaptor activity / protein stabilization / chromatin remodeling / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||
Authors | Willhoft O / Chua EYD | ||||||||||||||||||
Funding support | United Kingdom, 5 items
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Citation | Journal: Science / Year: 2018 Title: Structure and dynamics of the yeast SWR1-nucleosome complex. Authors: Oliver Willhoft / Mohamed Ghoneim / Chia-Liang Lin / Eugene Y D Chua / Martin Wilkinson / Yuriy Chaban / Rafael Ayala / Elizabeth A McCormack / Lorraine Ocloo / David S Rueda / Dale B Wigley / Abstract: The yeast SWR1 complex exchanges histone H2A in nucleosomes with Htz1 (H2A.Z in humans). The cryo-electron microscopy structure of the SWR1 complex bound to a nucleosome at 3.6-angstrom resolution ...The yeast SWR1 complex exchanges histone H2A in nucleosomes with Htz1 (H2A.Z in humans). The cryo-electron microscopy structure of the SWR1 complex bound to a nucleosome at 3.6-angstrom resolution reveals details of the intricate interactions between components of the SWR1 complex and its nucleosome substrate. Interactions between the Swr1 motor domains and the DNA wrap at superhelical location 2 distort the DNA, causing a bulge with concomitant translocation of the DNA by one base pair, coupled to conformational changes of the histone core. Furthermore, partial unwrapping of the DNA from the histone core takes place upon binding of nucleosomes to SWR1 complex. The unwrapping, as monitored by single-molecule data, is stabilized and has its dynamics altered by adenosine triphosphate binding but does not require hydrolysis. | ||||||||||||||||||
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_4396.map.gz | 12.8 MB | EMDB map data format | |
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Header (meta data) | emd-4396-v30.xml emd-4396.xml | 34.5 KB 34.5 KB | Display Display | EMDB header |
Images | emd_4396.png | 67.7 KB | ||
Filedesc metadata | emd-4396.cif.gz | 9.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4396 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4396 | HTTPS FTP |
-Validation report
Summary document | emd_4396_validation.pdf.gz | 226.2 KB | Display | EMDB validaton report |
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Full document | emd_4396_full_validation.pdf.gz | 225.3 KB | Display | |
Data in XML | emd_4396_validation.xml.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4396 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4396 | HTTPS FTP |
-Related structure data
Related structure data | 6genMC 4395C 6gejC 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_4396.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Chromatin remodeller-nucleosome complex at 4.5 A resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 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 : SWR1-nucleosome complex
+Supramolecule #1: SWR1-nucleosome complex
+Supramolecule #2: Histones
+Supramolecule #3: DNA
+Supramolecule #4: remodeller
+Macromolecule #1: Vacuolar protein sorting-associated protein 72
+Macromolecule #2: Histone H3
+Macromolecule #3: Histone H4
+Macromolecule #4: Histone H2A.1
+Macromolecule #5: Histone H2B.1
+Macromolecule #8: Helicase SWR1
+Macromolecule #9: Actin-like protein ARP6
+Macromolecule #10: Vacuolar protein sorting-associated protein 71
+Macromolecule #11: RuvB-like protein 1
+Macromolecule #12: RuvB-like protein 2
+Macromolecule #6: DNA (173-MER)
+Macromolecule #7: DNA (173-MER)
+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #14: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #15: MAGNESIUM ION
+Macromolecule #16: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL | ||||||||||||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.2 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 5517 / Average exposure time: 1.0 sec. / Average electron dose: 1.71794871794872 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0) / Number images used: 98529 |
Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 0.6.5) |
Final angle assignment | Type: OTHER / Software - Name: RELION (ver. 2.1.0) |