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- EMDB-6815: NuA4 TEEAA-Piccolo Complex -

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Basic information

Entry
Database: EMDB / ID: 6815
TitleNuA4 TEEAA-Piccolo Complex
Map data
SampleNuA4 TEEAA-Piccolo complex:
Function / homologyHistone acetyltransferase Esa1/KAT5/Tip60 / Chromo-like domain superfamily / RNA binding activity-knot of a chromodomain / MOZ/SAS family / MYST, zinc finger domain / Chromo/chromo shadow domain / Chromatin modification-related protein Yng2/Png1 / Zinc finger, PHD-type / Histone acetyltransferase domain, MYST-type / Inhibitor of growth proteins N-terminal histone-binding ...Histone acetyltransferase Esa1/KAT5/Tip60 / Chromo-like domain superfamily / RNA binding activity-knot of a chromodomain / MOZ/SAS family / MYST, zinc finger domain / Chromo/chromo shadow domain / Chromatin modification-related protein Yng2/Png1 / Zinc finger, PHD-type / Histone acetyltransferase domain, MYST-type / Inhibitor of growth proteins N-terminal histone-binding / Zinc finger, FYVE/PHD-type / MYST family zinc finger domain / Zinc finger, RING/FYVE/PHD-type / Chromatin modification-related protein Eaf6 / Zinc finger PHD-type signature. / Acyl-CoA N-acyltransferase / Enhancer of polycomb-like, N-terminal / Histone acetyltransferase subunit NuA4 / Zinc finger, PHD-type, conserved site / Zinc finger, PHD-finger / Inhibitor of growth protein, N-terminal histone-binding / Zinc finger PHD-type profile. / MYST-type histone acetyltransferase (HAT) domain profile. / Enhancer of polycomb protein / DNA Damage/Telomere Stress Induced Senescence / HATs acetylate histones / Sensing of DNA Double Strand Breaks / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Regulation of TP53 Activity through Acetylation / RNA binding activity-knot of a chromodomain / Estrogen-dependent gene expression / Winged helix-like DNA-binding domain superfamily / Enhancer of polycomb-like / NuA3b histone acetyltransferase complex / covalent chromatin modification / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / Piccolo NuA4 histone acetyltransferase complex / histone H4-K12 acetylation / histone displacement / histone H3-K14 acetylation / histone H2A acetylation / DNA-templated transcription, elongation / H4 histone acetyltransferase activity / histone H3-K23 acetylation / peptidyl-lysine acetylation / NuA4 histone acetyltransferase complex / peptide N-acetyltransferase activity / histone H4-K8 acetylation / histone H4-K5 acetylation / positive regulation of macroautophagy / histone acetyltransferase complex / MOZ/MORF histone acetyltransferase complex / histone acetylation / chromatin silencing at rDNA / histone acetyltransferase / histone acetyltransferase activity / methylated histone binding / positive regulation of transcription elongation from RNA polymerase II promoter / regulation of cell cycle / meiotic cell cycle / histone binding / nuclear chromatin / cell cycle / regulation of transcription by RNA polymerase II / DNA repair / negative regulation of transcription, DNA-templated / nucleolus / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus / cytosol / Chromatin modification-related protein YNG2 / Enhancer of polycomb-like protein 1 / Chromatin modification-related protein EAF6 / Histone acetyltransferase ESA1
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 7.6 Å resolution
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
DateDeposition: Aug 18, 2017 / Header (metadata) release: Apr 18, 2018 / Map release: Apr 18, 2018 / Last update: Apr 18, 2018

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Structure visualization

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

Downloads & links

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Map

Fileemd_6815.map.gz (map file in CCP4 format, 95552 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
1.3 Å/pix.
= 374.4 Å
288 pix
1.3 Å/pix.
= 374.4 Å
288 pix
1.3 Å/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
Contour Level:0.0166 (by author), 0.017 (movie #1):
Minimum - Maximum-0.0538694 - 0.10688296
Average (Standard dev.)0.0003114214 (0.003709165)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin0.00.00.0
Limit287.0287.0287.0
Spacing288288288
CellA=B=C: 374.4 Å
α=β=γ: 90.0 deg.

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 / Number of components: 1

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Component #1: protein, NuA4 TEEAA-Piccolo complex

ProteinName: NuA4 TEEAA-Piccolo complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 19060
3D reconstructionResolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF

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