4QUT

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 

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.,Université Grenoble Alpes/CNRS/CEA, Institut de Biologie Structurale, 38027 Grenoble, France.,CNAG-Centre for Genomic Regulation (CRG), Baldiri Reixac 4, 08028 Barcelona; Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIRI, International Center for Infectiology Research, EVIR team, INSERM U1111, CNRS, UMR5308, Université de Lyon-1, ENS de Lyon, Lyon, France INSERM, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), équipe 'contrôle métabolique des morts cellulaires', Nice 06204, France.,CIRI, International Center for Infectiology Research, EVIR team, INSERM U1111, CNRS, UMR5308, Université de Lyon-1, ENS de Lyon, Lyon, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, CEN Saclay, 91191 Gif-sur-Yvette, France.,Nuffield Department of Clinical Medicine, University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK Nuffield Department of Clinical Medicine, University of Oxford, Target Discovery Institute (TDI), NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK.,Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer Gasse 5-11, A-1121 Vienna, Austria.,The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA.,INSERM, U892; Centre de Recherche sur le Cancer Nantes Angers and UMR_S 892; Université d'Angers; Plateforme SNP, Transcriptome & Epigénomique; Centre Hospitalier Universitaire d'Angers, Angers 49000, France.,INSERM, U823; Université Grenoble Alpes; Institut Albert Bonniot Grenoble, F-38700 Grenoble, France khochbin@ujf-grenoble.fr.,The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA.




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
8Homo 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: 1.7 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.980α = 90.00
b = 78.980β = 90.00
c = 139.020γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

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