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Yorodumi- EMDB-32374: Cryo-EM structure of nucleosome in complex with p300 acetyltransf... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32374 | |||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex II) | |||||||||||||||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | p300 / nucleosome / acetyltransferase / GENE REGULATION | |||||||||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Hatazawa S / Liu J / Takizawa Y / Zandian M / Negishi L / Kutateladze TG / Kurumizaka H | |||||||||||||||||||||||||||||||||||||||
Funding support | Japan, United States, 12 items
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Citation | Journal: iScience / Year: 2022 Title: Structural basis for binding diversity of acetyltransferase p300 to the nucleosome. Authors: Suguru Hatazawa / Jiuyang Liu / Yoshimasa Takizawa / Mohamad Zandian / Lumi Negishi / Tatiana G Kutateladze / Hitoshi Kurumizaka / Abstract: p300 is a human acetyltransferase that associates with chromatin and mediates vital cellular processes. We now report the cryo-electron microscopy structures of the p300 catalytic core in complex ...p300 is a human acetyltransferase that associates with chromatin and mediates vital cellular processes. We now report the cryo-electron microscopy structures of the p300 catalytic core in complex with the nucleosome core particle (NCP). In the most resolved structure, the HAT domain and bromodomain of p300 contact nucleosomal DNA at superhelical locations 2 and 3, and the catalytic site of the HAT domain are positioned near the N-terminal tail of histone H4. Mutations of the p300-DNA interfacial residues of p300 substantially decrease binding to NCP. Three additional classes of p300-NCP complexes show different modes of the p300-NCP complex formation. Our data provide structural details critical to our understanding of the mechanism by which p300 acetylates multiple sites on the nucleosome. | |||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32374.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-32374-v30.xml emd-32374.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32374_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_32374.png | 72.3 KB | ||
Filedesc metadata | emd-32374.cif.gz | 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32374 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32374 | HTTPS FTP |
-Validation report
Summary document | emd_32374_validation.pdf.gz | 400 KB | Display | EMDB validaton report |
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Full document | emd_32374_full_validation.pdf.gz | 399.6 KB | Display | |
Data in XML | emd_32374_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_32374_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32374 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32374 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32374.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Nucleosome in complex with p300 acetyltransferase catalytic core ...
Entire | Name: Nucleosome in complex with p300 acetyltransferase catalytic core (complex I) |
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Components |
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-Supramolecule #1: Nucleosome in complex with p300 acetyltransferase catalytic core ...
Supramolecule | Name: Nucleosome in complex with p300 acetyltransferase catalytic core (complex I) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 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: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |