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Yorodumi- EMDB-51247: Structure of a mononucleosome bound by one copy of Chd1 with the ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-51247 | |||||||||
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Title | Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. | |||||||||
Map data | Mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA | |||||||||
Sample |
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Keywords | chromatin / remodeling / transcription / nucleosome / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / SAGA complex / sister chromatid cohesion ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / SAGA complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / site of double-strand break / histone binding / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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_51247.map.gz | 171.2 MB | EMDB map data format | |
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Header (meta data) | emd-51247-v30.xml emd-51247.xml | 26.1 KB 26.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_51247_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_51247.png | 103.2 KB | ||
Masks | emd_51247_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-51247.cif.gz | 7.7 KB | ||
Others | emd_51247_additional_1.map.gz emd_51247_half_map_1.map.gz emd_51247_half_map_2.map.gz | 201 MB 172.2 MB 172.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-51247 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-51247 | HTTPS FTP |
-Validation report
Summary document | emd_51247_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_51247_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_51247_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_51247_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51247 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51247 | HTTPS FTP |
-Related structure data
Related structure data | 9gd3MC 9gd0C 9gd1C 9gd2C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_51247.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA | ||||||||||||||||||||||||||||||||||||
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_51247_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: sharpened map
File | emd_51247_additional_1.map | ||||||||||||
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Annotation | sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_51247_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_51247_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad d...
+Supramolecule #1: Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad d...
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: Chromo domain-containing protein 1
+Macromolecule #5: DNA (231-MER)
+Macromolecule #6: DNA (231-MER)
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #9: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #10: MAGNESIUM ION
-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: 44.0 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 |