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- EMDB-6815: NuA4 TEEAA-Piccolo Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6815
TitleNuA4 TEEAA-Piccolo Complex
Map data
Sample
  • Complex: NuA4 TEEAA-Piccolo complex
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity ...PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / SUMOylation of transcription cofactors / DNA-templated transcription elongation / positive regulation of triglyceride biosynthetic process / histone H4 acetyltransferase activity / rDNA heterochromatin formation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / peptide N-acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / NuA4 histone acetyltransferase complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / methylated histone binding / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / nucleosome / regulation of cell cycle / chromatin remodeling / cell cycle / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleus / metal ion binding / cytosol
Similarity search - Function
Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / Enhancer of polycomb protein / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type ...Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / Enhancer of polycomb protein / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / Zinc finger, PHD-type, conserved site / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chromatin modification-related protein YNG2 / Enhancer of polycomb-like protein 1 / Chromatin modification-related protein EAF6 / Histone acetyltransferase ESA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 7.6 Å
AuthorsCai G / Wang X
CitationJournal: Nat Commun / Year: 2018
Title: Architecture of the Saccharomyces cerevisiae NuA4/TIP60 complex.
Authors: Xuejuan Wang / Salar Ahmad / Zhihui Zhang / Jacques Côté / Gang Cai /
Abstract: The NuA4/TIP60 acetyltransferase complex is required for gene regulation, DNA repair and cell cycle progression. The limited structural information impeded understanding of NuA4/TIP60 assembly and ...The NuA4/TIP60 acetyltransferase complex is required for gene regulation, DNA repair and cell cycle progression. The limited structural information impeded understanding of NuA4/TIP60 assembly and regulatory mechanism. Here, we report the 4.7 Å cryo-electron microscopy (cryo-EM) structure of a NuA4/TIP60 TEEAA assembly (Tra1, Eaf1, Eaf5, actin and Arp4) and the 7.6 Å cryo-EM structure of a TEEAA-piccolo assembly (Esa1, Epl1, Yng2 and Eaf6). The Tra1 and Eaf1 constitute the assembly scaffold. The Eaf1 SANT domain tightly binds to the LBE and FATC domains of Tra1 by ionic interactions. The actin/Arp4 peripherally associates with Eaf1 HSA domain. The Eaf5/7/3 (TINTIN) and piccolo modules largely pack against the FAT and HEAT repeats of Tra1 and their association depends on Eaf1 N-terminal and HSA regions, respectively. These structures elucidate the detailed architecture and molecular interactions between NuA4 subunits and offer exciting insights into the scaffolding and regulatory mechanisms of Tra1 pseudokinase.
History
DepositionAug 18, 2017-
Header (metadata) releaseApr 18, 2018-
Map releaseApr 18, 2018-
UpdateApr 18, 2018-
Current statusApr 18, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6815.png

Downloads & links

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Map

FileDownload / File: emd_6815.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 288 pix.
= 374.4 Å		1.3 Å/pix.
x 288 pix.
= 374.4 Å		1.3 Å/pix.
x 288 pix.
= 374.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0166 / Movie #1: 0.017
Minimum - Maximum-0.0538694 - 0.10688296
Average (Standard dev.)0.0003114214 (±0.003709165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z374.400374.400374.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0540.1070.000

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Supplemental data

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Sample components

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Entire : NuA4 TEEAA-Piccolo complex

EntireName: NuA4 TEEAA-Piccolo complex
Components
  • Complex: NuA4 TEEAA-Piccolo complex

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Supramolecule #1: NuA4 TEEAA-Piccolo complex

SupramoleculeName: NuA4 TEEAA-Piccolo complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: POSITIVE / Material: Uranyl Formate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19060
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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