Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16057.17 
• Atom Count: 1125 
• Residue Count: 136 
• Unique protein chains: 2

4TT2

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

• DOI: 10.2210/pdb4TT2/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2014-06-19 Released: 2014-12-24 
• Deposition Author(s): Poncet-Montange, G., Zhan, Y., Bardenhagen, J., Petrocchi, A., Leo, E., Shi, X., Lee, G., Leonard, P., Geck Do, M., Cardozo, M., Palmer, W., Andersen, J., Jones, P., Ladbury, J.

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Experimental Data Snapshot

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

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

• PubMed: 25486442 
• DOI: 10.1042/BJ20140933
• Primary Citation of Related Structures:  
  4TU6, 4TU4, 4TTE, 4TT6, 4TT4


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
ATPase family AAA domain-containing protein 2	A	130	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Histone H4K5Ac	P	6	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	P	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

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 = 77.550	α = 90.00
b = 77.550	β = 90.00
c = 62.440	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
MOLREP	phasing
iMOSFLM	data reduction
Blu-Ice	data collection
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-19 
• Released Date: 2014-12-24 
• Deposition Author(s): Poncet-Montange, G., Zhan, Y., Bardenhagen, J., Petrocchi, A., Leo, E., Shi, X., Lee, G., Leonard, P., Geck Do, M., Cardozo, M., Palmer, W., Andersen, J., Jones, P., Ladbury, J.

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