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- PDB-7vvy: TRA module of NuA4 -

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Basic information

Entry
Database: PDB / ID: 7vvy
TitleTRA module of NuA4
Components
  • Actin
  • Actin-related protein 4
  • Chromatin modification-related protein EAF1
  • Enhancer of polycomb-like protein 1
  • SWR1-complex protein 4
  • Transcription-associated protein 1
KeywordsDNA BINDING PROTEIN / NuA4 Tra1
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 / Swr1 complex / SLIK (SAGA-like) complex ...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 / kinetochore assembly / Ino80 complex / SAGA complex / SWI/SNF complex / establishment of cell polarity / NuA4 histone acetyltransferase complex / actin filament bundle / positive regulation of macroautophagy / protein secretion / chromosome organization / 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 / transcription corepressor activity / nucleosome / chromatin organization / histone binding / protein-containing complex assembly / hydrolase activity / chromatin remodeling / cell cycle / DNA repair / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative 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 / Transcription-associated protein 1 / Enhancer of polycomb-like protein 1 / SWR1-complex protein 4 / Actin / Actin-related protein 4 / Chromatin modification-related protein EAF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen, Z. / Qu, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Structure of the NuA4 acetyltransferase complex bound to the nucleosome.
Authors: Keke Qu / Kangjing Chen / Hao Wang / Xueming Li / Zhucheng Chen /
Abstract: Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an ...Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an important role in the formation of high-order chromatin structure and heterochromatin silencing. NuA4 in yeast and its homologue Tip60 complex in mammalian cells are the key enzymes that catalyse H4 acetylation, which in turn regulates chromatin packaging and function in transcription activation and DNA repair. Here we report the cryo-electron microscopy structure of NuA4 from Saccharomyces cerevisiae bound to the nucleosome. NuA4 comprises two major modules: the catalytic histone acetyltransferase (HAT) module and the transcription activator-binding (TRA) module. The nucleosome is mainly bound by the HAT module and is positioned close to a polybasic surface of the TRA module, which is important for the optimal activity of NuA4. The nucleosomal linker DNA carrying the upstream activation sequence is oriented towards the conserved, transcription activator-binding surface of the Tra1 subunit, which suggests a potential mechanism of NuA4 to act as a transcription co-activator. The HAT module recognizes the disk face of the nucleosome through the H2A-H2B acidic patch and nucleosomal DNA, projecting the catalytic pocket of Esa1 to the N-terminal tail of H4 and supporting its function in selective acetylation of H4. Together, our findings illustrate how NuA4 is assembled and provide mechanistic insights into nucleosome recognition and transcription co-activation by a HAT.
History
DepositionNov 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Chromatin modification-related protein EAF1
F: Actin-related protein 4
G: Actin
K: SWR1-complex protein 4
H: Enhancer of polycomb-like protein 1
L: Transcription-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)817,50810
Polymers816,4456
Non-polymers1,0634
Water00
1


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

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Components

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Protein , 6 types, 6 molecules EFGKHL

#1: Protein Chromatin modification-related protein EAF1 / ESA1-associated factor 1 / Vacuolar import and degradation protein 21


Mass: 133949.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: EAF1, VID21, YDR359C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06337
#2: Protein Actin-related protein 4 / Actin-like protein ARP4 / Actin-like protein 4


Mass: 54894.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: ARP4, ACT3, YJL081C, J1012 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P80428
#3: Protein Actin


Mass: 41735.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: ACT1, ABY1, END7, YFL039C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P60010
#4: Protein SWR1-complex protein 4 / ESA1-associated factor 2


Mass: 55297.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SWC4, EAF2, GOD1, YGR002C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53201
#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 S288C (yeast) / 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 , 2 types, 4 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / 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: TRA1 module of NuA4 / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69770 / Symmetry type: POINT

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