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- PDB-7yfp: The NuA4 histone acetyltransferase complex from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 7yfp
TitleThe NuA4 histone acetyltransferase complex from S. cerevisiae
Components
  • ARP4 isoform 1
  • Actin
  • Chromatin modification-related protein EAF1
  • Enhancer of polycomb-like protein 1
  • SWR1-complex protein 4
  • Transcription-associated protein 1
KeywordsTRANSFERASE / histone acetyltransferase / H4 / acetylation / NuA4 / nucleosome
Function / homology
Function and homology information


: / RHOB GTPase cycle / : / RHOA GTPase cycle / cellular bud neck contractile ring / piccolo histone acetyltransferase complex / ascospore wall assembly / vacuole inheritance / actin cortical patch / mitotic actomyosin contractile ring contraction ...: / RHOB GTPase cycle / : / RHOA GTPase cycle / cellular bud neck contractile ring / piccolo histone acetyltransferase complex / ascospore wall assembly / vacuole inheritance / actin cortical patch / mitotic actomyosin contractile ring contraction / Swr1 complex / SLIK (SAGA-like) complex / Ino80 complex / SAGA complex / intracellular non-membrane-bounded organelle / establishment of cell polarity / NuA4 histone acetyltransferase complex / actin filament bundle / positive regulation of macroautophagy / protein secretion / Ub-specific processing proteases / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / nucleosome / chromatin organization / hydrolase activity / chromatin remodeling / cell cycle / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus
Similarity search - Function
SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Enhancer of polycomb protein / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains ...SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / SANT/Myb-like domain of DAMP1 / Enhancer of polycomb protein / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / Myb-like domain profile. / domain in helicases and associated with SANT domains / Myb-like DNA-binding domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / PIK-related kinase, FAT / FAT domain / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Homeobox-like domain superfamily / ATPase, nucleotide binding domain / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ARP4 isoform 1 / SWR1-complex protein 4 / Chromatin modification-related protein EAF1 / Transcription-associated protein 1 / Enhancer of polycomb-like protein 1 / Actin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsJi, L.T. / Zhao, L.X. / Xu, K. / Gao, H.H. / Zhou, Y. / Kornberg, R.D. / Zhang, H.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structure of the NuA4 histone acetyltransferase complex.
Authors: Liting Ji / Lixia Zhao / Ke Xu / Huihan Gao / Yang Zhou / Roger D Kornberg / Heqiao Zhang /
Abstract: Nucleosome acetyltransferase of H4 (NuA4), one of two major histone acetyltransferase complexes in  specifically acetylates histone H2A and H4, resulting in increased transcriptional activity. Here ...Nucleosome acetyltransferase of H4 (NuA4), one of two major histone acetyltransferase complexes in  specifically acetylates histone H2A and H4, resulting in increased transcriptional activity. Here we present a 3.8-4.0 Å resolution structure of the NuA4 complex from cryoelectron microscopy and associated biochemical studies. The determined structure comprises six subunits and appropriately 5,000 amino acids, with a backbone formed by subunits Eaf1 and Eaf2 spanning from an Actin-Arp4 module to a platform subunit Tra1. Seven subunits are missing from the cryo-EM map. The locations of missing components, Yaf9, and three subunits of the Piccolo module Esa1, Yng2, and Eaf6 were determined. Biochemical studies showed that the Piccolo module and the complete NuA4 exhibit comparable histone acetyltransferase activities, but the Piccolo module binds to nucleosomes, whereas the complete NuA4 does not. The interaction lifetime of NuA4 and nucleosome is evidently short, possibly because of subunits of the NuA4 complex that diminish the affinity of the Piccolo module for the nucleosome, enabling rapid movement from nucleosome to nucleosome.
History
DepositionJul 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin
B: ARP4 isoform 1
D: Chromatin modification-related protein EAF1
E: SWR1-complex protein 4
F: Enhancer of polycomb-like protein 1
T: Transcription-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)794,4637
Polymers793,9566
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 6 molecules ABDEFT

#1: Protein Actin


Mass: 41402.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ACT1, ABY1, END7, YFL039C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P60010
#2: Protein ARP4 isoform 1


Mass: 54021.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ARP4, GI527_G0003169 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PX31
#3: Protein Chromatin modification-related protein EAF1


Mass: 112667.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EAF1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H8UNQ6
#4: Protein SWR1-complex protein 4


Mass: 55297.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SWC4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4F9Y4
#5: Protein Enhancer of polycomb-like protein 1


Mass: 96889.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EPL1, YFL024C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P43572
#6: Protein Transcription-associated protein 1


Mass: 433677.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38811

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The NuA4 histone acetyltransferase complex / Type: COMPLEX / Entity ID: #1-#4, #6, #5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197044 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 5OJS

5ojs


Accession code: 5OJS / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00541846
ELECTRON MICROSCOPYf_angle_d0.72156666
ELECTRON MICROSCOPYf_dihedral_angle_d18.0215455
ELECTRON MICROSCOPYf_chiral_restr0.0446397
ELECTRON MICROSCOPYf_plane_restr0.0057199

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