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- EMDB-32158: NCP-RA of NuA4 bound to the nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-32158
TitleNCP-RA of NuA4 bound to the nucleosome
Map dataNCP-RA cryo-EM density of NuA4
Sample
  • Complex: NuA4-NCP-acidic patch
    • Protein or peptide: NCP-RA
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChen Z / Qu K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Structure of the NuA4 acetyltransferase complex bound to the nucleosome.
Authors: Keke Qu / Kangjing Chen / Hao Wang / Xueming Li / Zhucheng Chen /
Abstract: Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an ...Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an important role in the formation of high-order chromatin structure and heterochromatin silencing. NuA4 in yeast and its homologue Tip60 complex in mammalian cells are the key enzymes that catalyse H4 acetylation, which in turn regulates chromatin packaging and function in transcription activation and DNA repair. Here we report the cryo-electron microscopy structure of NuA4 from Saccharomyces cerevisiae bound to the nucleosome. NuA4 comprises two major modules: the catalytic histone acetyltransferase (HAT) module and the transcription activator-binding (TRA) module. The nucleosome is mainly bound by the HAT module and is positioned close to a polybasic surface of the TRA module, which is important for the optimal activity of NuA4. The nucleosomal linker DNA carrying the upstream activation sequence is oriented towards the conserved, transcription activator-binding surface of the Tra1 subunit, which suggests a potential mechanism of NuA4 to act as a transcription co-activator. The HAT module recognizes the disk face of the nucleosome through the H2A-H2B acidic patch and nucleosomal DNA, projecting the catalytic pocket of Esa1 to the N-terminal tail of H4 and supporting its function in selective acetylation of H4. Together, our findings illustrate how NuA4 is assembled and provide mechanistic insights into nucleosome recognition and transcription co-activation by a HAT.
History
DepositionNov 11, 2021-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32158.png

Downloads & links

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Map

FileDownload / File: emd_32158.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNCP-RA cryo-EM density of NuA4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 376 pix.
= 407.02 Å		1.08 Å/pix.
x 376 pix.
= 407.02 Å		1.08 Å/pix.
x 376 pix.
= 407.02 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.022782851 - 0.08206916
Average (Standard dev.)5.1818864e-05 (±0.0011349882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 407.02 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NuA4-NCP-acidic patch

EntireName: NuA4-NCP-acidic patch
Components
  • Complex: NuA4-NCP-acidic patch
    • Protein or peptide: NCP-RA

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Supramolecule #1: NuA4-NCP-acidic patch

SupramoleculeName: NuA4-NCP-acidic patch / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: NCP-RA

MacromoleculeName: NCP-RA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK MPEPAKSAP APKKGSKKAV TKTQKKDGKK RRKSRKESYA ...String:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK MPEPAKSAP APKKGSKKAV TKTQKKDGKK RRKSRKESYA IYVYKVLKQV HPDTGISSKA MSIMNSFVND VFERIAGEAS RLAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK MA RTKQTARKST GGKAPRKQLA TKAARKSAPA TGGVKKPHRY RPGTVALREI RRYQKSTELL IRKLPFQRLV REIAQDFKTD LRFQSSAVMA LQEASEAYLV ALFEDTNLCA IHAKRVTIMP KDIQLARRIR GERA MSGRG KGGKGLGKGG AKRHRKVLRD NIQGITKPAI RRLARRGGVK RISGLIYEET RGVLKVFLEN VIRDAVTYTE HAKRKTVTAM DVVYALKRQG RTLYGFGG

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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: 7.6
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (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: 1.8 µm / Nominal defocus min: 1.2 µm

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 393016
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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