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- EMDB-60547: The architecture of human NuA4/TIP60-nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60547
TitleThe architecture of human NuA4/TIP60-nucleosome complex
Map dataoverall map of human TIP60-NCP complex
Sample
  • Complex: the architecture of human TIP60-nucleosome complex
KeywordsRemodeler / Histone Acetyltransferase Complex / NuA4 / TIP60 / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.4 Å
AuthorsChen K / Wang L / Yu Z / Yu J / Ren Y / Wang Q / Xu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Structure of the human TIP60 complex.
Authors: Ke Chen / Li Wang / Zishuo Yu / Jiali Yu / Yulei Ren / Qianmin Wang / Yanhui Xu /
Abstract: Mammalian TIP60 is a multi-functional enzyme with histone acetylation and histone dimer exchange activities. It plays roles in diverse cellular processes including transcription, DNA repair, cell ...Mammalian TIP60 is a multi-functional enzyme with histone acetylation and histone dimer exchange activities. It plays roles in diverse cellular processes including transcription, DNA repair, cell cycle control, and embryonic development. Here we report the cryo-electron microscopy structures of the human TIP60 complex with the core subcomplex and TRRAP module refined to 3.2-Å resolution. The structures show that EP400 acts as a backbone integrating the motor module, the ARP module, and the TRRAP module. The RUVBL1-RUVBL2 hexamer serves as a rigid core for the assembly of EP400 ATPase and YL1 in the motor module. In the ARP module, an ACTL6A-ACTB heterodimer and an extra ACTL6A make hydrophobic contacts with EP400 HSA helix, buttressed by network interactions among DMAP1, EPC1, and EP400. The ARP module stably associates with the motor module but is flexibly tethered to the TRRAP module, exhibiting a unique feature of human TIP60. The architecture of the nucleosome-bound human TIP60 reveals an unengaged nucleosome that is located between the core subcomplex and the TRRAP module. Our work illustrates the molecular architecture of human TIP60 and provides architectural insights into how this complex is bound by the nucleosome.
History
DepositionJun 14, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60547.png

Downloads & links

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Map

FileDownload / File: emd_60547.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoverall map of human TIP60-NCP complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.56 Å/pix.
x 80 pix.
= 444.8 Å		5.56 Å/pix.
x 80 pix.
= 444.8 Å		5.56 Å/pix.
x 80 pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.124316834 - 0.25737703
Average (Standard dev.)-0.008116988 (±0.018735208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 444.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The core subcomplex of human TIP60-NCP complex

Fileemd_60547_additional_1.map
AnnotationThe core subcomplex of human TIP60-NCP complex
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: The NCP-containing module of human TIP60-NCP complex

Fileemd_60547_additional_2.map
AnnotationThe NCP-containing module of human TIP60-NCP complex
Projections & Slices
AxesZYX

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Additional map: The TRRAP module of human TIP60-NCP complex

Fileemd_60547_additional_3.map
AnnotationThe TRRAP module of human TIP60-NCP complex
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: human TIP60-NCP complex overall half map2

Fileemd_60547_half_map_1.map
Annotationhuman TIP60-NCP complex overall half map2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : the architecture of human TIP60-nucleosome complex

EntireName: the architecture of human TIP60-nucleosome complex
Components
  • Complex: the architecture of human TIP60-nucleosome complex

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Supramolecule #1: the architecture of human TIP60-nucleosome complex

SupramoleculeName: the architecture of human TIP60-nucleosome complex / type: complex / ID: 1 / Parent: 0
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35936
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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