5J9W

Crystal structure of the NuA4 core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

    MOE Key Laboratory of Protein Science, Tsinghua University, Beijing 100086, China; School of Life Science, Tsinghua University, Beijing 100086, 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, C, K
280Saccharomyces 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
H, D, L
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download SDF File 
Download CCD File 
E, I
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
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: 2.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.260α = 90.00
b = 138.570β = 97.11
c = 167.868γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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