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Yorodumi- EMDB-9720: the crosslinked complex of ISWI-nucleosome in the ADP-bound state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9720 | |||||||||
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Title | the crosslinked complex of ISWI-nucleosome in the ADP-bound state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | chromatin remodelling / single particle CryO-EM / nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information Isw1b complex / Isw1 complex / Isw1a complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding / ATP-dependent chromatin remodeler activity / sister chromatid cohesion ...Isw1b complex / Isw1 complex / Isw1a complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding / ATP-dependent chromatin remodeler activity / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / nucleosome binding / ATP-dependent activity, acting on DNA / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / nucleosome / response to heat / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Xenopus laevis (African clawed frog) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Yan LJ / Wu H | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling. Authors: Lijuan Yan / Hao Wu / Xuemei Li / Ning Gao / Zhucheng Chen / Abstract: Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) ...Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) structures of Saccharomyces cerevisiae ISWI (ISW1) in complex with the nucleosome in adenosine diphosphate (ADP)-bound and ADP-BeF-bound states. The data show that after nucleosome binding, ISW1 is activated by substantial rearrangement of the catalytic domains, with the regulatory AutoN domain packing the first RecA-like core and the NegC domain being disordered. The high-resolution structure reveals local DNA distortion and translocation induced by ISW1 in the ADP-bound state, which is essentially identical to that induced by the Snf2 chromatin remodeler, suggesting a common mechanism of DNA translocation. The histone core remains largely unperturbed, and prevention of histone distortion by crosslinking did not inhibit the activity of yeast ISW1 or its human homolog. Together, our findings suggest a general mechanism of chromatin remodeling involving local DNA distortion without notable histone deformation. | |||||||||
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_9720.map.gz | 48.9 MB | EMDB map data format | |
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Header (meta data) | emd-9720-v30.xml emd-9720.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
Images | emd_9720.png | 217.5 KB | ||
Filedesc metadata | emd-9720.cif.gz | 7.1 KB | ||
Others | emd_9720_additional.map.gz | 2.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9720 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9720 | HTTPS FTP |
-Related structure data
Related structure data | 6iroMC 9718C 9719C 6jylC 6k1pC 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_9720.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_9720_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : the crosslinked complex of ISWI-nucleosome in the ADP-bound state
+Supramolecule #1: the crosslinked complex of ISWI-nucleosome in the ADP-bound state
+Supramolecule #2: ISW1
+Supramolecule #3: histone octamer
+Supramolecule #4: DNA
+Macromolecule #1: ISWI chromatin-remodeling complex ATPase ISW1
+Macromolecule #2: Histone H3
+Macromolecule #3: Histone H4
+Macromolecule #4: Histone H2A
+Macromolecule #5: Histone H2B 1.1
+Macromolecule #6: DNA (167-MER)
+Macromolecule #7: DNA (167-MER)
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 8.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.5 e/Å2 |
-Image processing
Startup model | Type of model: EMDB MAP |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168430 |