7VVZ

NuA4 bound to the nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the NuA4 acetyltransferase complex bound to the nucleosome.

Qu, K.Chen, K.Wang, H.Li, X.Chen, Z.

(2022) Nature 610: 569-574

  • DOI: 10.1038/s41586-022-05303-x
  • Primary Citation of Related Structures:  
    7VVU, 7VVY, 7VVZ

  • PubMed Abstract: 
  • Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes 1 , 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 2-4 ...

    Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes 1 , 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 2-4 . 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 5-10 . 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.


    Organizational Affiliation

    Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, P. R. China. zhucheng_chen@tsinghua.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin modification-related protein EAF6A [auth Y]113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EAF6YJR082CJ1854
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin modification-related protein YNG2B [auth V]282Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YNG2EAF4NBN1YHR090C
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Enhancer of polycomb-like protein 1T [auth H],
C [auth T]
832Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EPL1YFL024C
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3H [auth A],
D [auth O]
136Xenopus laevisMutation(s): 0 
Gene Names: LOC121398065LOC108703785LOC121398067
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4I [auth B],
E [auth Q]
103Xenopus laevisMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AJ [auth N],
F [auth S]
130Xenopus laevisMutation(s): 0 
Gene Names: h2ac14.Lh2ac14hist1h2ajhist1h2aj.LLOC494591
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1K [auth D],
G [auth U]
126Xenopus laevisMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase ESA1L [auth P]445Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ESA1YOR244WO5257
EC: 2.3.1.48 (UniProt), 2.3.1 (UniProt)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Epl1 arginine anchorO [auth X]9Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin modification-related protein EAF1P [auth E]1,168Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EAF1VID21YDR359C
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 4Q [auth F]489Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARP4ACT3YJL081CJ1012
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
ActinR [auth G]375Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ACT1ABY1END7YFL039C
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Entity ID: 15
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SWR1-complex protein 4S [auth K]476Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWC4EAF2GOD1YGR002C
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription-associated protein 1U [auth L]3,744Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsLengthOrganismImage
DNA (207-mer)M [auth W]207Saccharomyces cerevisiae
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Entity ID: 10
MoleculeChainsLengthOrganismImage
DNA (207-mer)N [auth I]207Saccharomyces cerevisiae
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMC (Subject of Investigation/LOI)
Query on CMC

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V [auth B]CARBOXYMETHYL COENZYME *A
C23 H38 N7 O18 P3 S
OBUOSIHPWVNVJN-GRFIIANRSA-N
 Ligand Interaction
ATP (Subject of Investigation/LOI)
Query on ATP

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X [auth F],
Z [auth G]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

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W [auth F],
Y [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2022-11-02
    Changes: Database references
  • Version 1.3: 2022-11-16
    Changes: Database references, Source and taxonomy, Structure summary