4QUU

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells.

Morozumi, Y.Boussouar, F.Tan, M.Chaikuad, A.Jamshidikia, M.Colak, G.He, H.Nie, L.Petosa, C.de Dieuleveult, M.Curtet, S.Vitte, A.L.Rabatel, C.Debernardi, A.Cosset, F.L.Verhoeyen, E.Emadali, A.Schweifer, N.Gianni, D.Gut, M.Guardiola, P.Rousseaux, S.Gerard, M.Knapp, S.Zhao, Y.Khochbin, S.

(2015) J Mol Cell Biol --: --

  • DOI: 10.1093/jmcb/mjv060
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although the conserved AAA ATPase and bromodomain factor, ATAD2, has been described as a transcriptional co-activator upregulated in many cancers, its function remains poorly understood. Here, using a combination of ChIP-seq, ChIP-proteomics, and RNA ...

    Although the conserved AAA ATPase and bromodomain factor, ATAD2, has been described as a transcriptional co-activator upregulated in many cancers, its function remains poorly understood. Here, using a combination of ChIP-seq, ChIP-proteomics, and RNA-seq experiments in embryonic stem cells where Atad2 is normally highly expressed, we found that Atad2 is an abundant nucleosome-bound protein present on active genes, associated with chromatin remodelling, DNA replication, and DNA repair factors. A structural analysis of its bromodomain and subsequent investigations demonstrate that histone acetylation guides ATAD2 to chromatin, resulting in an overall increase of chromatin accessibility and histone dynamics, which is required for the proper activity of the highly expressed gene fraction of the genome. While in exponentially growing cells Atad2 appears dispensable for cell growth, in differentiating ES cells Atad2 becomes critical in sustaining specific gene expression programmes, controlling proliferation and differentiation. Altogether, this work defines Atad2 as a facilitator of general chromatin-templated activities such as transcription.


    Organizational Affiliation

    INSERM, U823; Université Grenoble Alpes; Institut Albert Bonniot Grenoble, F-38700 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATPase family AAA domain-containing protein 2
A
130Homo sapiensMutation(s): 0 
Gene Names: ATAD2
EC: 3.6.1.3
Find proteins for Q6PL18 (Homo sapiens)
Go to Gene View: ATAD2
Go to UniProtKB:  Q6PL18
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B
14Homo sapiensMutation(s): 0 
Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.169 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.201α = 90.00
b = 79.201β = 90.00
c = 139.141γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
CrystalCleardata collection
MOSFLMdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2016-04-06
    Type: Database references