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- EMDB-32374: Cryo-EM structure of nucleosome in complex with p300 acetyltransf... -

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Basic information

Entry
Database: EMDB / ID: EMD-32374
TitleCryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex II)
Map data
Sample
  • Complex: Nucleosome in complex with p300 acetyltransferase catalytic core (complex I)
Keywordsp300 / nucleosome / acetyltransferase / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsHatazawa S / Liu J / Takizawa Y / Zandian M / Negishi L / Kutateladze TG / Kurumizaka H
Funding support Japan, United States, 12 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K06522 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101076 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101115j0004 Japan
Japan Science and TechnologyJPMJER1901 Japan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135671 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM125195 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA252707 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG067664 United States
Japan Agency for Medical Research and Development (AMED)JP22ama121009 Japan
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL151334 United States
CitationJournal: 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
DepositionDec 10, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32374.png

Downloads & links

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Map

FileDownload / File: emd_32374.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0049
Minimum - Maximum-0.022020519 - 0.05798839
Average (Standard dev.)0.00027714248 (±0.0022397242)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Nucleosome in complex with p300 acetyltransferase catalytic core ...

EntireName: Nucleosome in complex with p300 acetyltransferase catalytic core (complex I)
Components
  • Complex: Nucleosome in complex with p300 acetyltransferase catalytic core (complex I)

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Supramolecule #1: Nucleosome in complex with p300 acetyltransferase catalytic core ...

SupramoleculeName: Nucleosome in complex with p300 acetyltransferase catalytic core (complex I)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Å2
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:

3lz0

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145147
FSC plot (resolution estimation)

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