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- PDB-8x2x: The piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-... -

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Basic information

Entry
Database: PDB / ID: 8x2x
TitleThe piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state
Components
  • Chromatin modification-related protein
  • DNA (146-MER)
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • Histone acetyltransferase
  • Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6
  • glutathione transferase,Enhancer of polycomb-like protein
KeywordsGENE REGULATION / Nua4 / nucleosome
Function / homology
Function and homology information


: / NuA4 histone acetyltransferase complex / histone acetyltransferase activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / rRNA transcription / glutathione transferase / histone acetyltransferase complex / glutathione transferase activity ...: / NuA4 histone acetyltransferase complex / histone acetyltransferase activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / rRNA transcription / glutathione transferase / histone acetyltransferase complex / glutathione transferase activity / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / histone acetyltransferase / glutathione metabolic process / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / outer membrane-bounded periplasmic space / 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 / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / 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 / 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 / Histone-fold / Thioredoxin-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Chromatin modification-related protein EAF6 / Histone H2B / Histone H4 / Histone acetyltransferase ESA1 / Histone H3 / : / : ...DNA / DNA (> 10) / DNA (> 100) / Chromatin modification-related protein EAF6 / Histone H2B / Histone H4 / Histone acetyltransferase ESA1 / Histone H3 / : / : / : / Maltose/maltodextrin-binding periplasmic protein / glutathione transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
Schistosoma japonicum (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang, L. / Zhang, H. / Zhu, H. / Zhu, P.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Mar 19, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6
N: Chromatin modification-related protein
K: Histone acetyltransferase
M: glutathione transferase,Enhancer of polycomb-like protein
I: DNA (146-MER)
J: DNA (146-MER)
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B


Theoretical massNumber of molelcules
Total (without water)398,76214
Polymers398,76214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 12 molecules LNKMAEBFCGDH

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Chromatin modification-related protein EAF6


Mass: 59471.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: K12 / Gene: malE, EAF6
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0AEX9, UniProt: A0A6A5PYU5
#2: Protein Chromatin modification-related protein


Mass: 13828.894 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YNG2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A8H4C0Q6
#3: Protein Histone acetyltransferase


Mass: 55419.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ESA1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6A5Q414
#4: Protein glutathione transferase,Enhancer of polycomb-like protein


Mass: 69285.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GSTM1, EPL1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q540A3, UniProt: A0A8H8UL58
#6: Protein Histone H3


Mass: 15391.007 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HHT2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6A5Q536
#7: Protein Histone H4


Mass: 11338.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HHF1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6A5Q1V3
#8: Protein Histone H2A


Mass: 14313.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HTZ1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6A5Q818
#9: Protein Histone H2B


Mass: 14280.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HTB1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6A5PZQ7

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DNA chain , 1 types, 2 molecules IJ

#5: DNA chain DNA (146-MER)


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Details

Has protein modificationN

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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 piccolo NuA4 bound to the H2A.Z nucleosome complex at pre-H4-acetylation state
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10 mM HEPES,50 mM Nacl
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22283 / Symmetry type: POINT

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