5J9Q

Crystal structure of the NuA4 core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  

  • 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 cryoelectr ...

    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

    State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100086, China.,School of Life Science, Tsinghua University, Beijing 100086, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: zhup@ibp.ac.cn.,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.,MOE Key Laboratory of Protein Science, Tsinghua University, Beijing 100086, China; School of Life Science, Tsinghua University, Beijing 100086, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase ESA1
E, A, I
305Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: ESA1
EC: 2.3.1.48
Find proteins for Q08649 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08649
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Chromatin modification-related protein EAF6
F, B, J
113Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EAF6
Find proteins for P47128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47128
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Enhancer of polycomb-like protein 1
G, N, C
351Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EPL1
Find proteins for P43572 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43572
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Chromatin modification-related protein YNG2
D, H, K
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: YNG2 (EAF4, NBN1)
Find proteins for P38806 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38806
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Htz1
L, M, O
10Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HTZ1 (H2AZ, HTA3)
Find proteins for Q12692 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12692
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
A, E, I
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.250 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 217.857α = 90.00
b = 190.990β = 113.56
c = 172.346γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2014CB910100

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Author supporting evidence, Database references, Derived calculations