4TT4 | pdb_00004tt4

Crystal structure of ATAD2A bromodomain complexed with H3(1-21)K14Ac peptide

• PDB DOI: https://doi.org/10.2210/pdb4TT4/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 2.70 Å
• R-Value Free: 
  0.240 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1042/BJ20140933
• Primary Citation Related Structures: 
  4TT2, 4TT4, 4TT6, 4TTE, 4TU4, 4TU6


• 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.
†Department of Biochemistry and Molecular Biology and Center for Biomolecular Structure and Function, The University of Texas MD Anderson Cancer Center, Unit 1000, 1515 Holcombe Boulevard, Houston TX 77030, U.S.A.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.85 kDa 
• Atom Count: 2,309 
• Modeled Residue Count: 265 
• Deposited Residue Count: 265 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family AAA domain-containing protein 2	A, B	130	Homo sapiens	Mutation(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 GTEx:  ENSG00000156802

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3(1-21)K4Ac	C [auth P]	5	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.240 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.16	α = 90
b = 115.68	β = 90
c = 77.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• 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: 2015-03-04
  Changes: Database references
• Version 2.0: 2022-04-13
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Refinement description
• Version 2.2: 2023-11-15
  Changes: Data collection
• Version 2.3: 2024-11-20
  Changes: Structure summary