+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9719 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The complex of ISWI-nucleosome in the ADP.BeF-bound state | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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 / negative regulation of RNA export from nucleus / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding ...Isw1b complex / Isw1 complex / Isw1a complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of RNA export from nucleus / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / nucleosome binding / ATP-dependent activity, acting on DNA / helicase activity / mRNA 3'-UTR binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / nucleosome / nucleosome assembly / response to heat / transcription cis-regulatory region binding / chromatin remodeling / hydrolase activity / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / 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: 3.87 Å | |||||||||
Authors | Yan LJ / Wu H / Li XM / Gao N / Chen ZC | |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9719.map.gz | 38 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-9719-v30.xml emd-9719.xml | 24.9 KB 24.9 KB | Display Display | EMDB header |
Images | emd_9719.png | 181.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9719 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9719 | HTTPS FTP |
-Validation report
Summary document | emd_9719_validation.pdf.gz | 467.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_9719_full_validation.pdf.gz | 467.4 KB | Display | |
Data in XML | emd_9719_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_9719_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9719 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9719 | HTTPS FTP |
-Related structure data
Related structure data | 6k1pMC 9718C 9720C 6iroC 6jylC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_9719.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : the complex of ISWI-nucleosome in the ADP-BeF-bound state
+Supramolecule #1: the complex of ISWI-nucleosome in the ADP-BeF-bound state
+Supramolecule #2: ISW1
+Supramolecule #3: nuleosome
+Supramolecule #4: DNA
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: ISWI chromatin-remodeling complex ATPase ISW1
+Macromolecule #5: DNA (167-MER)
+Macromolecule #6: DNA (167-MER)
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #9: BERYLLIUM TRIFLUORIDE ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Concentration | 0.1 mg/mL |
---|---|
Buffer | pH: 8.5 / Component - Concentration: 1.35 mg/ml / Component - Formula: NaCl / Component - Name: sodium chloride / Details: 10 mM Tris 50 mM NaCl |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 20.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa / Details: no special treatment |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 1.5s. |
Details | monodisperse |
-Electron microscopy
Microscope | FEI TITAN |
---|---|
Temperature | Min: 100.0 K / Max: 100.0 K |
Details | performed manually |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 29000 / Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 5000 |
Sample stage | Specimen holder model: GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: HELIUM |
-Image processing
CTF correction | Software - Name: RELION (ver. 3.0) |
---|---|
Final reconstruction | Number classes used: 5 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Details: relion / Number images used: 62121 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0) |