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- EMDB-34590: Cryo-EM structure of the p300 catalytic core bound to the H4K12ac... -

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Basic information

Entry
Database: EMDB / ID: EMD-34590
TitleCryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (3.9 angstrom resolution)
Map data
Sample
  • Complex: the p300 catalytic core bound to the H4K12acK16ac nucleosome
KeywordsAcetyl taransferase / Complex / Nucleosome / TRANSFERASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKikuchi M / Morita S / Wakamori M / Sato S / Uchikubo-Kamo T / Shirouzu M / Umehara T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: 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
DepositionOct 26, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34590.png

Downloads & links

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Map

FileDownload / File: emd_34590.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 340 pix.
= 281.86 Å		0.83 Å/pix.
x 340 pix.
= 281.86 Å		0.83 Å/pix.
x 340 pix.
= 281.86 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.0064397566 - 0.029261677
Average (Standard dev.)0.0000594566 (±0.0015883393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 281.86 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34590_msk_1.map
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Half map: #1

Fileemd_34590_half_map_1.map
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Half map: #2

Fileemd_34590_half_map_2.map
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Sample components

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Entire : the p300 catalytic core bound to the H4K12acK16ac nucleosome

EntireName: the p300 catalytic core bound to the H4K12acK16ac nucleosome
Components
  • Complex: the p300 catalytic core bound to the H4K12acK16ac nucleosome

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Supramolecule #1: the p300 catalytic core bound to the H4K12acK16ac nucleosome

SupramoleculeName: 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.
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1kx3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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