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: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.3 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.

(2016) J Mol Cell Biol 8: 349-362

  • DOI: https://doi.org/10.1093/jmcb/mjv060
  • Primary Citation of Related Structures:  
    4QUT, 4QUU

  • 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-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 ...

    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 khochbin@ujf-grenoble.fr.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase family AAA domain-containing protein 2130Homo sapiensMutation(s): 0 
Gene Names: ATAD2, L16, PRO2000
EC: 3.6.1.3 (PDB Primary Data), 3.6.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens)
Explore Q6PL18 
Go to UniProtKB:  Q6PL18
PHAROS:  Q6PL18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PL18
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H48Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
Entity Groups  
UniProt GroupP62805
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.98α = 90
b = 78.98β = 90
c = 139.02γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2016-04-06
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-20
    Changes: Data collection, Refinement description