5J9W

Crystal structure of the NuA4 core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

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Literature

The NuA4 Core Complex Acetylates Nucleosomal Histone H4 through a Double Recognition Mechanism

Xu, P.Li, C.Chen, Z.Jiang, S.Fan, S.Wang, J.Dai, J.Zhu, P.Chen, Z.

(2016) Mol Cell 63: 965-975

  • DOI: https://doi.org/10.1016/j.molcel.2016.07.024
  • Primary Citation of Related Structures:  
    5J9Q, 5J9T, 5J9U, 5J9W

  • PubMed Abstract: 

    NuA4 catalyzes the acetylation of nucleosomes at histone H4, which is a well-established epigenetic event, controlling many genomic processes in Saccharomyces cerevisiae. Here we report the crystal structures of the NuA4 core complex and a cryoelectron microscopy structure with the nucleosome. The structures show that the histone-binding pocket of the enzyme is rearranged, suggesting its activation. The enzyme binds the histone tail mainly through the target lysine residue, with a preference for a small residue at the -1 position. The complex engages the nucleosome at the dish face and orients its catalytic pocket close to the H4 tail to achieve selective acetylation. The combined data reveal a space-sequence double recognition mechanism of the histone tails by a modifying enzyme in the context of the nucleosome.


  • Organizational Affiliation

    MOE Key Laboratory of Protein Science, Tsinghua University, Beijing 100086, China; School of Life Science, Tsinghua University, Beijing 100086, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase ESA1A [auth E],
E [auth A],
I
305Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: ESA1YOR244WO5257
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for Q08649 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ08649
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin modification-related protein EAF6B [auth F],
F [auth B],
J
113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EAF6YJR082CJ1854
UniProt
Find proteins for P47128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Enhancer of polycomb-like protein 1C [auth G],
G [auth C],
K
280Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EPL1YFL024C
UniProt
Find proteins for P43572 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP43572
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin modification-related protein YNG2D [auth H],
H [auth D],
L
120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YNG2EAF4NBN1YHR090C
UniProt
Find proteins for P38806 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
A [auth E],
E [auth A],
I
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.26α = 90
b = 138.57β = 97.11
c = 167.868γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ACOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary