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- PDB-7vvz: NuA4 bound to the nucleosome -

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Entry
Database: PDB / ID: 7vvz
TitleNuA4 bound to the nucleosome
Components
  • (Chromatin modification-related protein ...) x 3
  • (DNA (207-mer)) x 2
  • Actin
  • Actin-related protein 4
  • Enhancer of polycomb-like protein 1
  • Epl1 arginine anchor
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • Histone acetyltransferase ESA1
  • SWR1-complex protein 4
  • Transcription-associated protein 1
KeywordsDNA BINDING PROTEIN/DNA / NuA4 nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Regulation of TP53 Activity through Acetylation / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / NuA3b histone acetyltransferase complex / PI5P Regulates TP53 Acetylation / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / cellular bud neck contractile ring ...Regulation of TP53 Activity through Acetylation / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / NuA3b histone acetyltransferase complex / PI5P Regulates TP53 Acetylation / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / Gap junction degradation / RHOA GTPase cycle / piccolo histone acetyltransferase complex / vacuole inheritance / TTT Hsp90 cochaperone complex / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / ascospore wall assembly / Platelet degranulation / positive regulation of triglyceride biosynthetic process / protein localization to nuclear inner membrane / actin cortical patch / SUMOylation of transcription cofactors / SLIK (SAGA-like) complex / histone H4 acetyltransferase activity / Swr1 complex / rDNA heterochromatin formation / SAGA complex / Ino80 complex / histone H3K4me3 reader activity / SWI/SNF complex / kinetochore assembly / establishment of cell polarity / histone acetyltransferase activity / DNA-templated transcription elongation / actin filament bundle / NuA4 histone acetyltransferase complex / protein secretion / positive regulation of macroautophagy / DNA repair-dependent chromatin remodeling / chromosome organization / protein-lysine-acetyltransferase activity / histone acetyltransferase / nucleosomal DNA binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / actin filament / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / meiotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / structural constituent of chromatin / transcription corepressor activity / actin cytoskeleton / nucleosome / chromatin organization / heterochromatin formation / protein-containing complex assembly / histone binding / protein-macromolecule adaptor activity / regulation of cell cycle / chromatin remodeling / protein heterodimerization activity / DNA repair / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA-templated transcription / DNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / 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 / 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 / ING family ...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 / 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 / ING family / Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / : / 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 / Myb-like domain profile. / RNA binding activity-knot of a chromodomain / Myb-like DNA-binding domain / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / PIK-related kinase, FAT / FAT domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / Chromo-like domain superfamily / 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 / Zinc finger, PHD-type, conserved site / PHD-finger / Actins signature 1. / Actin, conserved site / Actins signature 2. / Acyl-CoA N-acyltransferase / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Zinc finger PHD-type signature. / Actin / Actin family / Actin / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Zinc finger, FYVE/PHD-type / Homeobox-like domain superfamily / Histone H3 signature 1. / ATPase, nucleotide binding domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CARBOXYMETHYL COENZYME *A / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B 1.1 / Chromatin modification-related protein YNG2 / SAGA complex/NuA4 acetyltransferase complex subunit TRA1 / Enhancer of polycomb-like protein 1 ...ADENOSINE-5'-TRIPHOSPHATE / CARBOXYMETHYL COENZYME *A / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B 1.1 / Chromatin modification-related protein YNG2 / SAGA complex/NuA4 acetyltransferase complex subunit TRA1 / Enhancer of polycomb-like protein 1 / Chromatin modification-related protein EAF6 / SWR1-complex protein 4 / Actin / Actin-related protein 4 / Chromatin modification-related protein EAF1 / Histone acetyltransferase ESA1 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Xenopus laevis (African clawed frog)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsQu, K. / Chen, Z.
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 1.3Nov 16, 2022Group: Database references / Source and taxonomy / Structure summary
Category: em_entity_assembly / entity ...em_entity_assembly / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _em_entity_assembly.source / _entity.pdbx_description ..._em_entity_assembly.source / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Y: Chromatin modification-related protein EAF6
V: Chromatin modification-related protein YNG2
T: Enhancer of polycomb-like protein 1
O: Histone H3
Q: Histone H4
S: Histone H2A
U: Histone H2B 1.1
A: Histone H3
B: Histone H4
N: Histone H2A
D: Histone H2B 1.1
P: Histone acetyltransferase ESA1
W: DNA (207-mer)
I: DNA (207-mer)
X: Epl1 arginine anchor
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)1,251,78626
Polymers1,249,89721
Non-polymers1,8895
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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Chromatin modification-related protein ... , 3 types, 3 molecules YVE

#1: Protein Chromatin modification-related protein EAF6


Mass: 12915.704 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: P47128
#2: Protein Chromatin modification-related protein YNG2


Mass: 32139.514 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: P38806
#12: Protein Chromatin modification-related protein EAF1


Mass: 133949.953 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: Q06337

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Protein , 10 types, 15 molecules THOAQBSNUDPFGKL

#3: Protein Enhancer of polycomb-like protein 1


Mass: 96889.867 Da / Num. of mol.: 2
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
#4: Protein Histone H3


Mass: 15435.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A310TTQ1
#5: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria)
#6: Protein Histone H2A


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h2ac14.L, h2ac14, hist1h2aj, hist1h2aj.L, LOC494591 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6AZJ8
#7: Protein Histone H2B 1.1 / H2B1.1


Mass: 13965.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02281
#8: Protein Histone acetyltransferase ESA1


Mass: 52692.844 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: Q08649
#13: 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
#14: 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
#15: 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
#16: 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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DNA chain , 2 types, 2 molecules WI

#9: DNA chain DNA (207-mer)


Mass: 63679.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#10: DNA chain DNA (207-mer)


Mass: 64150.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Protein/peptide , 1 types, 1 molecules X

#11: Protein/peptide Epl1 arginine anchor


Mass: 1175.449 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)

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Non-polymers , 3 types, 5 molecules

#17: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#19: 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
Has protein modificationY

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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 bound to the nucleosome / Type: COMPLEX / Entity ID: #1-#16 / Source: MULTIPLE SOURCES
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: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 474949 / Symmetry type: POINT

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