4TT2

Crystal structure of ATAD2A bromodomain complexed with H4(1-20)K5Ac peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2.

Poncet-Montange, G.Zhan, Y.Bardenhagen, J.P.Petrocchi, A.Leo, E.Shi, X.Lee, G.R.Leonard, P.G.Geck Do, M.K.Cardozo, M.G.Andersen, J.N.Palmer, W.S.Jones, P.Ladbury, J.E.

(2015) Biochem.J. 466: 337-346

  • DOI: 10.1042/BJ20140933
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Preventing histone recognition by bromodomains emerges as an attractive therapeutic approach in cancer. Overexpression of ATAD2 (ATPase family AAA domain-containing 2 isoform A) in cancer cells is associated with poor prognosis making the bromodomain ...

    Preventing histone recognition by bromodomains emerges as an attractive therapeutic approach in cancer. Overexpression of ATAD2 (ATPase family AAA domain-containing 2 isoform A) in cancer cells is associated with poor prognosis making the bromodomain of ATAD2 a promising epigenetic therapeutic target. In the development of an in vitro assay and identification of small molecule ligands, we conducted structure-guided studies which revealed a conformationally flexible ATAD2 bromodomain. Structural studies on apo-, peptide-and small molecule-ATAD2 complexes (by co-crystallization) revealed that the bromodomain adopts a 'closed', histone-compatible conformation and a more 'open' ligand-compatible conformation of the binding site respectively. An unexpected conformational change of the conserved asparagine residue plays an important role in driving the peptide-binding conformation remodelling. We also identified dimethylisoxazole-containing ligands as ATAD2 binders which aided in the validation of the in vitro screen and in the analysis of these conformational studies.


    Organizational Affiliation

    *Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Unit 1954, 1515 Holcombe Blvd, Houston, TX 77030, U.S.A.




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 H4K5Ac
P
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
P
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.550α = 90.00
b = 77.550β = 90.00
c = 62.440γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
iMOSFLMdata reduction
Blu-Icedata collection
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Derived calculations
  • Version 1.2: 2015-03-04
    Type: Database references
  • Version 2.0: 2017-11-22
    Type: Atomic model, Database references, Derived calculations, Other, Refinement description, Source and taxonomy