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- EMDB-60587: The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ complex witho... -

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Entry
Database: EMDB / ID: EMD-60587
TitleThe piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ complex without Ac-CoA at pre-H2A.Z-acetylation state
Map data
Sample
  • Complex: The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ complex without Ac-CoA at pre-H2A.Z-acetylation state
KeywordsNua4 / nucleosome / GENE REGULATION
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsWang L / Zhang H / Zhu H / Zhu P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)E2VK311RA1 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-EM structures reveal the acetylation process of piccolo NuA4.
Authors: Lin Wang / Haonan Zhang / Qi Jia / Wenyan Li / Chenguang Yang / Lijuan Ma / Ming Li / Ying Lu / Hongtao Zhu / Ping Zhu /
Abstract: NuA4 is the only essential acetyltransferase in yeast that can catalyze the acetylation of the histones H2A, H2A.Z, and H4, thereby affecting gene transcription. However, the acetylation process of ...NuA4 is the only essential acetyltransferase in yeast that can catalyze the acetylation of the histones H2A, H2A.Z, and H4, thereby affecting gene transcription. However, the acetylation process of NuA4, such as how NuA4 acetylates H4 and H2A.Z differently, remains largely elusive. Here, using cryoelectron microscopy (cryo-EM) single particle analysis, we present seven cryo-EM structures of piccolo NuA4 (pNuA4) in complex with wild-type H2A.Z or H2A.Z-mutant-containing nucleosomes in the absence or presence of acetyl coenzyme A (Ac-CoA). We revealed that, in the absence of Ac-CoA, pNuA4 adopts multiple conformations to search for its substrates. After adding Ac-CoA, the single-molecule Förster resonance energy transfer (smFRET) and cryo-EM data indicated that pNuA4 prefers to bind H4 and undergoes a dynamic conformational change to complete the acetylation. We also obtained previously unseen structures in states associated with the acetylation of H2A.Z. These cryo-EM structures and smFRET results suggest a complex acetylation process on H4 and H2A.Z by pNuA4. The results provide a comprehensive picture of the mechanism by which pNuA4 acetylates its substrates within an H2A.Z-containing nucleosome.
History
DepositionJun 18, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60587.png

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Map

FileDownload / File: emd_60587.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
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Contour LevelBy AUTHOR: 0.00838
Minimum - Maximum-0.003231691 - 0.025638934
Average (Standard dev.)0.00016061391 (±0.0015724023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60587_msk_1.map
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Half map: #1

Fileemd_60587_half_map_1.map
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Half map: #2

Fileemd_60587_half_map_2.map
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Sample components

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Entire : The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ complex witho...

EntireName: The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ complex without Ac-CoA at pre-H2A.Z-acetylation state
Components
  • Complex: The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ complex without Ac-CoA at pre-H2A.Z-acetylation state

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Supramolecule #1: The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ complex witho...

SupramoleculeName: The piccolo NuA4 bound to the H2A.Z nucleosome-H4KQ complex without Ac-CoA at pre-H2A.Z-acetylation state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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
VitrificationCryogen name: ETHANE
Details10 mM HEPES,50 mM Nacl

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2046
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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