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- PDB-7zvw: NuA4 Histone Acetyltransferase Complex -

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Basic information

Entry
Database: PDB / ID: 7zvw
TitleNuA4 Histone Acetyltransferase Complex
Components
  • (Actin) x 2
  • Chromatin modification-related protein EAF1
  • Enhancer of polycomb-like protein
  • SWR1-complex protein 4
  • Transcription-associated protein
KeywordsTRANSCRIPTION / NuA4 / histone acetyltransferase complex / Epigenetics / DNA repair
Function / homology
Function and homology information


: / : / piccolo histone acetyltransferase complex / : / Swr1 complex / Ino80 complex / kinetochore assembly / NuA4 histone acetyltransferase complex / positive regulation of macroautophagy / chromosome organization ...: / : / piccolo histone acetyltransferase complex / : / Swr1 complex / Ino80 complex / kinetochore assembly / NuA4 histone acetyltransferase complex / positive regulation of macroautophagy / chromosome organization / histone acetyltransferase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleosome / chromatin organization / histone binding / cytoskeleton / hydrolase activity / chromatin remodeling / DNA repair / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm
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 / 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 / Actin / Transcription-associated protein / SWR1-complex protein 4 / Enhancer of polycomb-like protein / Chromatin modification-related protein EAF1 / Actin
Similarity search - Component
Biological speciesKomagataella phaffii GS115 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSchultz, P. / Ben-Shem, A. / Frechard, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE12-0022 France
Citation
Journal: Nat Struct Mol Biol / Year: 2023
Title: The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification.
Authors: Alexander Fréchard / Céline Faux / Rozalie Hexnerova / Corinne Crucifix / Gabor Papai / Ekaterina Smirnova / Conor McKeon / Florie Lo Ying Ping / Dominique Helmlinger / Patrick Schultz / Adam Ben-Shem /
Abstract: Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa ...Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa NuA4 complex, which plays pivotal roles in both transcription and DNA-damage repair. NuA4 has the unique capacity to acetylate histone targets located several nucleosomes away from its recruitment site. Neither the molecular mechanism of this activity nor its physiological importance are known. Here we report the structure of the Pichia pastoris NuA4 complex, with its core resolved at 3.4-Å resolution. Three subunits, Epl1, Eaf1 and Swc4, intertwine to form a stable platform that coordinates all other modules. The HAT module is firmly anchored into the core while retaining the ability to stretch out over a long distance. We provide structural, biochemical and genetic evidence that an unfolded linker region of the Epl1 subunit is critical for this long-range activity. Specifically, shortening the Epl1 linker causes severe growth defects and reduced H4 acetylation levels over broad chromatin regions in fission yeast. Our work lays the foundations for a mechanistic understanding of NuA4's regulatory role and elucidates how its essential long-range activity is attained.
#1: Journal: Res Sq / Year: 2022
Title: The structure of the NuA4/Tip60 complex reveals the mechanism and importance of long-range chromatin modification
Authors: Schultz, P. / Frechard, A. / Hexnerova, R. / Crucifix, C. / Papai, G. / Smirnova, E. / Faux, C. / Ping, F. / Helmlinger, D. / Ben-Shem, A.
History
DepositionMay 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.name
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.3Sep 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)922,61511
Polymers921,5527
Non-polymers1,0634
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54540 Å2
ΔGint-328 kcal/mol
Surface area207190 Å2

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Components

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Protein , 6 types, 7 molecules ABGEHFC

#1: Protein Transcription-associated protein


Mass: 438055.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864 / References: UniProt: C4QYV4
#2: Protein Actin /


Mass: 41736.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864 / References: UniProt: Q9P4D1
#3: Protein Actin /


Mass: 53009.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864 / References: UniProt: C4QXM9
#4: Protein Chromatin modification-related protein EAF1 / ESA1-associated factor 1 / Vacuolar import and degradation protein 21


Mass: 118498.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864 / References: UniProt: C4R7G0
#5: Protein SWR1-complex protein 4


Mass: 64916.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864 / References: UniProt: C4R0G7
#6: Protein Enhancer of polycomb-like protein


Mass: 86836.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / Strain: GS115 / ATCC 20864 / References: UniProt: C4R6V1

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Non-polymers , 2 types, 4 molecules

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


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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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: NuA4 histone acetyltransferase complex / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Komagataella phaffii GS115 (fungus)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMPotassium acetateKOAc1
35 mMMagnesium acetateMgOAc1
42 mMtris(2-carboxyethyl)phosphineTCEP1
55 mMAmmonium acetateNH4OAc1
60.0025 %Dodecyl-maltosideDDM1
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3800 nm / Nominal defocus min: 1400 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1265830
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 518386 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00338472
ELECTRON MICROSCOPYf_angle_d0.58452245
ELECTRON MICROSCOPYf_dihedral_angle_d4.4995280
ELECTRON MICROSCOPYf_chiral_restr0.046006
ELECTRON MICROSCOPYf_plane_restr0.0046718

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