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- EMDB-38023: The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-38023
TitleThe class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state
Map data
Sample
  • Complex: The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone acetyltransferase
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6
    • Protein or peptide: glutathione transferase,Enhancer of polycomb-like protein
    • Protein or peptide: Chromatin modification-related protein
    • DNA: DNA (146-MER)
KeywordsNua4 / nucleosome / GENE REGULATION
Function / homology
Function and homology information


: / detection of maltose stimulus / maltose transport complex / NuA4 histone acetyltransferase complex / carbohydrate transport / glutathione transferase / rRNA transcription / histone acetyltransferase complex / glutathione transferase activity / carbohydrate transmembrane transporter activity ...: / detection of maltose stimulus / maltose transport complex / NuA4 histone acetyltransferase complex / carbohydrate transport / glutathione transferase / rRNA transcription / histone acetyltransferase complex / glutathione transferase activity / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / histone acetyltransferase activity / histone acetyltransferase / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / glutathione metabolic process / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / structural constituent of chromatin / nucleosome / nucleosome assembly / outer membrane-bounded periplasmic space / chromatin organization / periplasmic space / protein heterodimerization activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / DNA binding / nucleus / membrane
Similarity search - Function
Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / 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 / Glutathione S-transferase, C-terminal domain ...Chromatin modification-related protein Eaf6 / Histone acetyltransferase subunit NuA4 / 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 / Glutathione S-transferase, C-terminal domain / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Glutathione S-transferase, C-terminal domain superfamily / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Acyl-CoA N-acyltransferase / Histone H2B signature. / Histone H2B / Histone H2B / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Thioredoxin-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chromatin modification-related protein EAF6 / Histone H2B / Histone H4 / Histone acetyltransferase ESA1 / Histone H3 / : / : / : / Maltose/maltodextrin-binding periplasmic protein / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang L / Zhang H / Zhu H / Zhu P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)E2VK311RA1 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-EM structures reveal the acetylation process of piccolo NuA4.
Authors: Lin Wang / Haonan Zhang / Qi Jia / Wenyan Li / Chenguang Yang / Lijuan Ma / Ming Li / Ying Lu / Hongtao Zhu / Ping Zhu /
Abstract: NuA4 is the only essential acetyltransferase in yeast that can catalyze the acetylation of the histones H2A, H2A.Z, and H4, thereby affecting gene transcription. However, the acetylation process of ...NuA4 is the only essential acetyltransferase in yeast that can catalyze the acetylation of the histones H2A, H2A.Z, and H4, thereby affecting gene transcription. However, the acetylation process of NuA4, such as how NuA4 acetylates H4 and H2A.Z differently, remains largely elusive. Here, using cryoelectron microscopy (cryo-EM) single particle analysis, we present seven cryo-EM structures of piccolo NuA4 (pNuA4) in complex with wild-type H2A.Z or H2A.Z-mutant-containing nucleosomes in the absence or presence of acetyl coenzyme A (Ac-CoA). We revealed that, in the absence of Ac-CoA, pNuA4 adopts multiple conformations to search for its substrates. After adding Ac-CoA, the single-molecule Förster resonance energy transfer (smFRET) and cryo-EM data indicated that pNuA4 prefers to bind H4 and undergoes a dynamic conformational change to complete the acetylation. We also obtained previously unseen structures in states associated with the acetylation of H2A.Z. These cryo-EM structures and smFRET results suggest a complex acetylation process on H4 and H2A.Z by pNuA4. The results provide a comprehensive picture of the mechanism by which pNuA4 acetylates its substrates within an H2A.Z-containing nucleosome.
History
DepositionNov 10, 2023-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38023.png

Downloads & links

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Map

FileDownload / File: emd_38023.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-0.28884062 - 17.960256999999999
Average (Standard dev.)-0.019763771 (±0.470989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38023_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_38023_half_map_1.map
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Half map: #1

Fileemd_38023_half_map_2.map
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Sample components

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Entire : The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex ...

EntireName: The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state
Components
  • Complex: The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone acetyltransferase
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6
    • Protein or peptide: glutathione transferase,Enhancer of polycomb-like protein
    • Protein or peptide: Chromatin modification-related protein
    • DNA: DNA (146-MER)

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Supramolecule #1: The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex ...

SupramoleculeName: The class2 of piccolo NuA4 bound to the H2A.Z nucleosome complex at harboring state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 15.391007 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPH RYKPGTVALR EIRRFQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA IGALQESVEA YLVSLFEDTN LAAIHAKRVT IQKKDIKLAR RLRGERS

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 11.338338 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KILRDNIQGI TKPAIRRLAR RGGVKRISGL IYEEVRAVLK SFLESVIRDS VTYTEHAKRK TVTSLDVVY ALKRQGRTLY GFG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.313727 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGKAHGGKG KSGAKDSGSL RSQSSSARAG LQFPVGRIKR YLKRHATGRT RVGSKAAIYL TAVLEYLTAE VLELAGNAAK DLKVKRITP RHLQLAIRGD DELDSLIRAT IASGGVLPHI NKALLLKVEK KGSKK

UniProtKB: UNIPROTKB: A0A6A5Q818

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.280362 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSAKAEKKPA SKAPAEKKPA AKKTSTSTDG KKRSKARKET YSSYIYKVLK QTHPDTGISQ KSMSILNSFV NDIFERIATE ASKLAAYNK KSTISAREIQ TAVRLILPGE LAKHAVSEGT RAVTKYSSST QA

UniProtKB: Histone H2B

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Macromolecule #5: Histone acetyltransferase

MacromoleculeName: Histone acetyltransferase / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 55.419664 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SQDHENLYFQ GAGSMSHDGK EEPGIAKKIN SVDDIIIKCQ CWVQKNDEER LAEILSINTR KAPPKFYVHY VNYNKRLDE WITTDRINLD KEVLYPKLKA TDEDNKKQKK KKATNTSETP QDSLQDGVDG FSRENTDVMD LDNLNVQGIK D ENISHEDE ...String:
MGSSHHHHHH SQDHENLYFQ GAGSMSHDGK EEPGIAKKIN SVDDIIIKCQ CWVQKNDEER LAEILSINTR KAPPKFYVHY VNYNKRLDE WITTDRINLD KEVLYPKLKA TDEDNKKQKK KKATNTSETP QDSLQDGVDG FSRENTDVMD LDNLNVQGIK D ENISHEDE IKKLRTSGSM TQNPHEVARV RNLNRIIMGK YEIEPWYFSP YPIELTDEDF IYIDDFTLQY FGSKKQYERY RK KCTLRHP PGNEIYRDDY VSFFEIDGRK QRTWCRNLCL LSKLFLDHKT LYYDVDPFLF YCMTRRDELG HHLVGYFSKE KES ADGYNV ACILTLPQYQ RMGYGKLLIE FSYELSKKEN KVGSPEKPLS DLGLLSYRAY WSDTLITLLV EHQKEITIDE ISSM TSMTT TDILHTAKTL NILRYYKGQH IIFLNEDILD RYNRLKAKKR RTIDPNRLIW KPPVFTASQL RFAW

UniProtKB: Histone acetyltransferase ESA1

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Macromolecule #6: Maltose/maltodextrin-binding periplasmic protein,Chromatin modifi...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 59.471164 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKIKTGARIL ALSALTTMMF SASALAKIEE GKLVIWINGD KGYNGLAEVG KKFEKDTGIK VTVEHPDKLE EKFPQVAATG DGPDIIFWA HDRFGGYAQS GLLAEITPDK AFQDKLYPFT WDAVRYNGKL IAYPIAVEAL SLIYNKDLLP NPPKTWEEIP A LDKELKAK ...String:
MKIKTGARIL ALSALTTMMF SASALAKIEE GKLVIWINGD KGYNGLAEVG KKFEKDTGIK VTVEHPDKLE EKFPQVAATG DGPDIIFWA HDRFGGYAQS GLLAEITPDK AFQDKLYPFT WDAVRYNGKL IAYPIAVEAL SLIYNKDLLP NPPKTWEEIP A LDKELKAK GKSALMFNLQ EPYFTWPLIA ADGGYAFKYE NGKYDIKDVG VDNAGAKAGL TFLVDLIKNK HMNADTDYSI AE AAFNKGE TAMTINGPWA WSNIDTSKVN YGVTVLPTFK GQPSKPFVGV LSAGINAASP NKELAKEFLE NYLLTDEGLE AVN KDKPLG AVALKSYEEE LVKDPRIAAT MENAQKGEIM PNIPQMSAFW YAVRTAVINA ASGRQTVDEA LKDAQTNSSS NNNN NNNNN NLGIEGRISE FENLYFQGHM TDELKSYEAL KAELKKSLQD RREQEDTFDN LQQEIYDKET EYFSHNSNNN HSGHG GAHG SKSHYSGNII KGFDTFSKSH HSHADSAFNN NDRIFSLSSA TYVKQQHGQS QND

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Chromatin modification-related protein EAF6

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Macromolecule #7: glutathione transferase,Enhancer of polycomb-like protein

MacromoleculeName: glutathione transferase,Enhancer of polycomb-like protein
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 69.285969 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM CLDAFPKLVC FKKRIEAIPQ IDKYLKSSKY IAWPLQGWQA TFGGGDHPPK SDLVPRGSEN LYFQGHMSSN SR FRHRKIS VKQHLKIYLP NDLKHLDKDE LQQREVVEIE TGVEKNEEKE VHLHRILQMG SGHTKHKDYI PTPDASMTWN EYD KFYTGS FQETTSYIKF SATVEDCCGT NYNMDERDET FLNEQVNKGS SDILTEDEFE ILCSSFEHAI HERQPFLSMD PESI LSFEE LKPTLIKSDM ADFNLRNQLN HEINSHKTHF ITQFDPVSQM NTRPLIQLIE KFGSKIYDYW RERKIEVNGY EIFPQ LKFE RPGEKEEIDP YVCFRRREVR HPRKTRRIDI LNSQRLRALH QELKNAKDLA LLVAKRENVS LNWINDELKI FDQRVK IKN LKRSLNISGE DDDLINHKRK RPT

UniProtKB: Glutathione S-transferase class-mu 26 kDa isozyme, UNIPROTKB: A0A8H8UL58

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Macromolecule #8: Chromatin modification-related protein

MacromoleculeName: Chromatin modification-related protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.828894 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MDPSLVLEQT IQDVSNLPSE FRYLLEEIGS NDLKLIEEKK KYEQKESQIH KFIRQQGSIP KHPQEDGLDK EIKESLLKCQ SLQREKCVL ANTALFLIAR HLNKLEKNIA LLEEDGVLAP V

UniProtKB: UNIPROTKB: A0A8H4C0Q6

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Macromolecule #9: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 9 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 45.054844 KDa
SequenceString: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG) ...String:
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT) (DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG) (DG)(DC) (DA)(DT)(DG)(DT)(DT)(DC)(DA) (DG)(DC)(DG)(DG)(DA)(DA)(DT)(DT)(DC)(DC) (DG)(DC)(DT) (DG)(DA)(DA)(DC)(DA)(DT) (DG)(DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DG) (DC)(DA)(DG)(DT)(DT) (DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA) (DC)(DT)(DT)(DT)(DT) (DG)(DG)(DT)(DA) (DG)(DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG) (DG)(DT)(DG)(DG)(DA)(DT) (DA)(DT)(DT) (DG)(DA)(DT)

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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

BufferpH: 7
VitrificationCryogen name: ETHANE
Details10 mM HEPES,50 mM Nacl

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27187
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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