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- EMDB-9536: Structure of NuA4 core complex binds with the nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-9536
TitleStructure of NuA4 core complex binds with the nucleosome
Map data
Sample
  • Complex: NuA4 core complex with mono nucleosome
    • Other: NuA4 core complex with NCP
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / NuA3 histone acetyltransferase complex / piccolo histone acetyltransferase complex / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity ...PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / NuA3 histone acetyltransferase complex / 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 / peptide N-acetyltransferase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / peptide-lysine-N-acetyltransferase activity / NuA4 histone acetyltransferase complex / positive regulation of macroautophagy / Estrogen-dependent gene expression / 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 / DNA repair / 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 / 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 / Enhancer of polycomb protein / : / MYST, zinc finger domain / MYST family zinc finger domain ...Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / 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 / Enhancer of polycomb protein / : / 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 speciesPichia norvegensis (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsXu P / Li C / Chen Z / Jiang S / Fan S / Wang J / Dai J / Zhu P
CitationJournal: Mol Cell / Year: 2016
Title: The NuA4 Core Complex Acetylates Nucleosomal Histone H4 through a Double Recognition Mechanism.
Authors: Peng Xu / Chengmin Li / Zhihong Chen / Shuanying Jiang / Shilong Fan / Jiawei Wang / Junbiao Dai / Ping Zhu / Zhucheng Chen /
Abstract: NuA4 catalyzes the acetylation of nucleosomes at histone H4, which is a well-established epigenetic event, controlling many genomic processes in Saccharomyces cerevisiae. Here we report the crystal ...NuA4 catalyzes the acetylation of nucleosomes at histone H4, which is a well-established epigenetic event, controlling many genomic processes in Saccharomyces cerevisiae. Here we report the crystal structures of the NuA4 core complex and a cryoelectron microscopy structure with the nucleosome. The structures show that the histone-binding pocket of the enzyme is rearranged, suggesting its activation. The enzyme binds the histone tail mainly through the target lysine residue, with a preference for a small residue at the -1 position. The complex engages the nucleosome at the dish face and orients its catalytic pocket close to the H4 tail to achieve selective acetylation. The combined data reveal a space-sequence double recognition mechanism of the histone tails by a modifying enzyme in the context of the nucleosome.
History
DepositionAug 11, 2016-
Header (metadata) releaseSep 21, 2016-
Map releaseSep 21, 2016-
UpdateOct 19, 2016-
Current statusOct 19, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9536.png

Downloads & links

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Map

FileDownload / File: emd_9536.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 100 pix.
= 268. Å		2.68 Å/pix.
x 100 pix.
= 268. Å		2.68 Å/pix.
x 100 pix.
= 268. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.6 / Movie #1: 2.6
Minimum - Maximum-3.1868212 - 18.109725999999998
Average (Standard dev.)0.000000005810783 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.682.682.68
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z268.000268.000268.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-3.18718.1100.000

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Supplemental data

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Sample components

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Entire : NuA4 core complex with mono nucleosome

EntireName: NuA4 core complex with mono nucleosome
Components
  • Complex: NuA4 core complex with mono nucleosome
    • Other: NuA4 core complex with NCP

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Supramolecule #1: NuA4 core complex with mono nucleosome

SupramoleculeName: NuA4 core complex with mono nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Esa1, Yng2,Epl1,Eaf6,Widom-601,DNA,H2A,H2B,H3,H4
Source (natural)Organism: Pichia norvegensis (yeast)
Recombinant expressionOrganism: Escherichia coli O103:H2 str. 12009 (bacteria)
Molecular weightTheoretical: 320 kDa/nm

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Macromolecule #1: NuA4 core complex with NCP

MacromoleculeName: NuA4 core complex with NCP / type: other / ID: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid

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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

Concentration0.15 mg/mL
BufferpH: 7 / Component:
ConcentrationFormula
10.0 mMHEPES
50.0 mMNacl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsgradient fixation

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-34 / Average exposure time: 1.5 sec. / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52420
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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