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- EMDB-15066: NuA4 Histone Acetyltransferase complex - Upper lobe -

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Basic information

Entry
Database: EMDB / ID: EMD-15066
TitleNuA4 Histone Acetyltransferase complex - Upper lobe
Map data
Sample
  • Complex: NuA4 histone acetyltransferase complex
KeywordsNuA4 / histone acetyltransferase complex / Epigenetics / DNA repair / TRANSCRIPTION
Biological speciesKomagataella phaffii GS115 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsFrechard A / Hexnerova R / Crucifix C / Papai G / Smirnova E / Faux C / Lo Ying Ping F / Helmlinger D / Schultz P / Ben-shem A
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE12-0022 France
Citation
Journal: Nat Struct Mol Biol / Year: 2023
Title: The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification.
Authors: Alexander Fréchard / Céline Faux / Rozalie Hexnerova / Corinne Crucifix / Gabor Papai / Ekaterina Smirnova / Conor McKeon / Florie Lo Ying Ping / Dominique Helmlinger / Patrick Schultz / Adam Ben-Shem /
Abstract: Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa ...Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa NuA4 complex, which plays pivotal roles in both transcription and DNA-damage repair. NuA4 has the unique capacity to acetylate histone targets located several nucleosomes away from its recruitment site. Neither the molecular mechanism of this activity nor its physiological importance are known. Here we report the structure of the Pichia pastoris NuA4 complex, with its core resolved at 3.4-Å resolution. Three subunits, Epl1, Eaf1 and Swc4, intertwine to form a stable platform that coordinates all other modules. The HAT module is firmly anchored into the core while retaining the ability to stretch out over a long distance. We provide structural, biochemical and genetic evidence that an unfolded linker region of the Epl1 subunit is critical for this long-range activity. Specifically, shortening the Epl1 linker causes severe growth defects and reduced H4 acetylation levels over broad chromatin regions in fission yeast. Our work lays the foundations for a mechanistic understanding of NuA4's regulatory role and elucidates how its essential long-range activity is attained.
#1: Journal: Res Sq / Year: 2022
Title: The structure of the NuA4/Tip60 complex reveals the mechanism and importance of long-range chromatin modification
Authors: Schultz P / Frechard A / Hexnerova R / Crucifix C / Papai G / Smirnova E / Faux C / Ping F / Helmlinger D / Ben-Shem A
History
DepositionJun 1, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15066.png

Downloads & links

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Map

FileDownload / File: emd_15066.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 448 pix.
= 386.176 Å		0.86 Å/pix.
x 448 pix.
= 386.176 Å		0.86 Å/pix.
x 448 pix.
= 386.176 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 1.16
Minimum - Maximum-6.108463 - 5.7883162
Average (Standard dev.)0.0077589517 (±0.09047881)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 386.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15066_msk_1.map
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Half map: Half map B

Fileemd_15066_half_map_1.map
AnnotationHalf map B
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Half map: Half map A

Fileemd_15066_half_map_2.map
AnnotationHalf map A
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Sample components

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Entire : NuA4 histone acetyltransferase complex

EntireName: NuA4 histone acetyltransferase complex
Components
  • Complex: NuA4 histone acetyltransferase complex

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Supramolecule #1: NuA4 histone acetyltransferase complex

SupramoleculeName: NuA4 histone acetyltransferase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Komagataella phaffii GS115 (fungus)

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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

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMKOAcPotassium acetate
5.0 mMMgOAcMagnesium acetate
2.0 mMTCEPtris(2-carboxyethyl)phosphine
5.0 mMNH4OAcAmmonium acetate
0.0025 %DDMDodecyl-maltoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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: 3.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1265830
Startup modelType of model: OTHER / Details: cryoSPARC ab-initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 518386

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