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Yorodumi- EMDB-34590: Cryo-EM structure of the p300 catalytic core bound to the H4K12ac... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34590 | |||||||||
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Title | Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (3.9 angstrom resolution) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Acetyl taransferase / Complex / Nucleosome / TRANSFERASE | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Kikuchi M / Morita S / Wakamori M / Sato S / Uchikubo-Kamo T / Shirouzu M / Umehara T | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Epigenetic mechanisms to propagate histone acetylation by p300/CBP. Authors: Masaki Kikuchi / Satoshi Morita / Masatoshi Wakamori / Shin Sato / Tomomi Uchikubo-Kamo / Takehiro Suzuki / Naoshi Dohmae / Mikako Shirouzu / Takashi Umehara / Abstract: Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryogenic electron microscopy structures in which ...Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryogenic electron microscopy structures in which a p300/CREB-binding protein (CBP) multidomain monomer recognizes histone H4 N-terminal tail (NT) acetylation (ac) in a nucleosome and acetylates non-H4 histone NTs within the same nucleosome. p300/CBP not only recognized H4NTac via the bromodomain pocket responsible for reading, but also interacted with the DNA minor grooves via the outside of that pocket. This directed the catalytic center of p300/CBP to one of the non-H4 histone NTs. The primary target that p300 writes by reading H4NTac was H2BNT, and H2BNTac promoted H2A-H2B dissociation from the nucleosome. We propose a model in which p300/CBP replicates histone N-terminal tail acetylation within the H3-H4 tetramer to inherit epigenetic storage, and transcribes it from the H3-H4 tetramer to the H2B-H2A dimers to activate context-dependent gene transcription through local nucleosome destabilization. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34590.map.gz | 136.9 MB | EMDB map data format | |
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Header (meta data) | emd-34590-v30.xml emd-34590.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34590_fsc.xml | 12.1 KB | Display | FSC data file |
Images | emd_34590.png | 74.4 KB | ||
Masks | emd_34590_msk_1.map | 149.9 MB | Mask map | |
Others | emd_34590_half_map_1.map.gz emd_34590_half_map_2.map.gz | 118.2 MB 118.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34590 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34590 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34590.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.829 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34590_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34590_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_34590_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the p300 catalytic core bound to the H4K12acK16ac nucleosome
Entire | Name: the p300 catalytic core bound to the H4K12acK16ac nucleosome |
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Components |
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-Supramolecule #1: the p300 catalytic core bound to the H4K12acK16ac nucleosome
Supramolecule | Name: the p300 catalytic core bound to the H4K12acK16ac nucleosome type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / Details: p300 was expressed in insect cells. |
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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: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |