5J9T

Crystal structure of the NuA4 core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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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: 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 ...

    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. Electronic address: zhucheng_chen@tsinghua.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase ESA1E [auth A], A [auth E], I305Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: ESA1YOR244WO5257
EC: 2.3.1.48
UniProt
Find proteins for Q08649 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin modification-related protein EAF6F [auth B], B [auth F], J113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EAF6YJR082CJ1854
UniProt
Find proteins for P47128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Enhancer of polycomb-like protein 1G [auth C], C [auth G], K280Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EPL1YFL024C
UniProt
Find proteins for P43572 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin modification-related protein YNG2H [auth D], D [auth H], L120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YNG2EAF4NBN1YHR090C
UniProt
Find proteins for P38806 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38806 
Go to UniProtKB:  P38806
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
A [auth E], E [auth A], IL-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.685α = 90
b = 137.582β = 97.63
c = 168.076γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2016-04-11 
  • Released Date: 2016-10-26 
  • Deposition Author(s): Chen, Z.C., Xu, P.

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release