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Yorodumi- EMDB-51245: Original nucleosome portion of DN103, unsharpened focused refinement -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-51245 | |||||||||
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Title | Original nucleosome portion of DN103, unsharpened focused refinement | |||||||||
Map data | Original nucleosome portion, unsharpened focus refinement | |||||||||
Sample |
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Keywords | chromatin / remodeling / transcription / nucleosome / DNA BINDING PROTEIN | |||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Engeholm M / Roske JJ / Oberbeckmann E / Dienemann C / Lidschreiber M / Cramer P / Farnung L | |||||||||
Funding support | Germany, European Union, 2 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT. Authors: Maik Engeholm / Johann J Roske / Elisa Oberbeckmann / Christian Dienemann / Michael Lidschreiber / Patrick Cramer / Lucas Farnung / Abstract: To maintain the nucleosome organization of transcribed genes, ATP-dependent chromatin remodelers collaborate with histone chaperones. Here, we show that at the 5' ends of yeast genes, RNA polymerase ...To maintain the nucleosome organization of transcribed genes, ATP-dependent chromatin remodelers collaborate with histone chaperones. Here, we show that at the 5' ends of yeast genes, RNA polymerase II (RNAPII) generates hexasomes that occur directly adjacent to nucleosomes. The resulting hexasome-nucleosome complexes are then resolved by Chd1. We present two cryoelectron microscopy (cryo-EM) structures of Chd1 bound to a hexasome-nucleosome complex before and after restoration of the missing inner H2A/H2B dimer by FACT. Chd1 uniquely interacts with the complex, positioning its ATPase domain to shift the hexasome away from the nucleosome. In the absence of the inner H2A/H2B dimer, its DNA-binding domain (DBD) packs against the ATPase domain, suggesting an inhibited state. Restoration of the dimer by FACT triggers a rearrangement that displaces the DBD and stimulates Chd1 remodeling. Our results demonstrate how chromatin remodelers interact with a complex nucleosome assembly and suggest how Chd1 and FACT jointly support transcription by RNAPII. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_51245.map.gz | 64.5 MB | EMDB map data format | |
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Header (meta data) | emd-51245-v30.xml emd-51245.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_51245_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_51245.png | 34.4 KB | ||
Masks | emd_51245_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-51245.cif.gz | 4 KB | ||
Others | emd_51245_half_map_1.map.gz emd_51245_half_map_2.map.gz | 65.2 MB 65.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-51245 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-51245 | HTTPS FTP |
-Validation report
Summary document | emd_51245_validation.pdf.gz | 741.5 KB | Display | EMDB validaton report |
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Full document | emd_51245_full_validation.pdf.gz | 741 KB | Display | |
Data in XML | emd_51245_validation.xml.gz | 17 KB | Display | |
Data in CIF | emd_51245_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51245 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51245 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_51245.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Original nucleosome portion, unsharpened focus refinement | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.834 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_51245_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_51245_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_51245_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Entire | Name: Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. |
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Components |
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-Supramolecule #1: Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Supramolecule | Name: Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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: 57.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |