[English] 日本語
Yorodumi- EMDB-25483: 2.9 A structure of the nucleosome-bound ChEx, part of the chromat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25483 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 2.9 A structure of the nucleosome-bound ChEx, part of the chromatin remodeler Chd1 | |||||||||
Map data | Sharpened 2.9A map with a negative bfactor (-30) in an orientation aligned to a common reference. | |||||||||
Sample |
| |||||||||
Keywords | CHD1 / chromatin remodeling / ATPase / DBD / nucleosome / remodeling / transcription / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Nodelman IM / Das S / Faustino AM / Fried SD / Bowman GD / Armache J-P | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state. Authors: Ilana M Nodelman / Sayan Das / Anneliese M Faustino / Stephen D Fried / Gregory D Bowman / Jean-Paul Armache / Abstract: Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. Here we report a complex of the Chd1 remodeler bound to a nucleosome in a nucleotide-free ...Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. Here we report a complex of the Chd1 remodeler bound to a nucleosome in a nucleotide-free state, determined by cryo-EM to 2.3 Å resolution. The remodeler stimulates the nucleosome to absorb an additional nucleotide on each strand at two different locations: on the tracking strand within the ATPase binding site and on the guide strand one helical turn from the ATPase motor. Remarkably, the additional nucleotide on the tracking strand is associated with a local transformation toward an A-form geometry, explaining how sequential ratcheting of each DNA strand occurs. The structure also reveals a histone-binding motif, ChEx, which can block opposing remodelers on the nucleosome and may allow Chd1 to participate in histone reorganization during transcription. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25483.map.gz | 51.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-25483-v30.xml emd-25483.xml | 28.6 KB 28.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25483_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_25483.png | 103.1 KB | ||
Masks | emd_25483_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-25483.cif.gz | 5.3 KB | ||
Others | emd_25483_additional_1.map.gz emd_25483_additional_2.map.gz emd_25483_additional_3.map.gz emd_25483_additional_4.map.gz emd_25483_additional_5.map.gz emd_25483_half_map_1.map.gz emd_25483_half_map_2.map.gz | 37.4 MB 30.6 MB 64.3 MB 939.8 KB 2.6 MB 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25483 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25483 | HTTPS FTP |
-Related structure data
Related structure data | 7swyC 7tn2C C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10876 (Title: 2.3 A structure of the ATP-dependent chromatin remodeler Chd1 bound to the nucleosome in a nucleotide-free state Data size: 4.7 TB Data #1: Unaligned frames of Chd1-bound nucleosomes collected on Gatan K3 in Super Resolution [micrographs - multiframe] Data #2: MotionCor2-aligned frames of Chd1-bound nucleosomes collected on Gatan K3 [micrographs - single frame] Data #3: Processed subsets [picked particles - single frame - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_25483.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened 2.9A map with a negative bfactor (-30) in an orientation aligned to a common reference. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_25483_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened 2.9A map in an orientation aligned to a common reference.
File | emd_25483_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened 2.9A map in an orientation aligned to a common reference. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened 2.9A map
File | emd_25483_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened 2.9A map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Sharpened 2.9A map with a negative bfactor (-30)
File | emd_25483_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened 2.9A map with a negative bfactor (-30) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: FSC Mask from cryoSPARC (before auto-tightening)
File | emd_25483_additional_4.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | FSC Mask from cryoSPARC (before auto-tightening) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Refine Mask from cryoSPARC
File | emd_25483_additional_5.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Refine Mask from cryoSPARC | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half-map 1 (half A) from cryoSPARC
File | emd_25483_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half-map 1 (half_A) from cryoSPARC | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half-map 2 (half B) from cryoSPARC
File | emd_25483_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half-map 2 (half_B) from cryoSPARC | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a...
Entire | Name: Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state |
---|---|
Components |
|
-Supramolecule #1: Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a...
Supramolecule | Name: Chd1 ATP-dependent chromatin remodeler bound to a nucleosome in a nucleotide-free state type: complex / ID: 1 / Parent: 0 / Details: This entry has a weak DNA-binding domain |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 400 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.7 mg/mL |
---|---|
Buffer | pH: 7 Details: 20 mM HEPES, pH 7.0, 60 mM KCl, 1.5 mM DTT, 1 mM MgCl2 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | Nucleosome-bound CHD1, prepared in the presence of ATPgammaS, and then crosslinked using GraFix. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 28.0 µm / Calibrated defocus min: 4.0 µm / Calibrated magnification: 46296 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -2.2 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 6906 / Average exposure time: 3.3 sec. / Average electron dose: 49.9 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |