ATAD2B bromodomain in complex with histone H4 acetylated at lysine 12

Experimental Data Snapshot

  • Resolution: 1.92 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report

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Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains.

Phillips, M.Malone, K.L.Boyle, B.W.Montgomery, C.Kressy, I.A.Joseph, F.M.Bright, K.M.Boyson, S.P.Chang, S.Nix, J.C.Young, N.L.Jeffers, V.Frietze, S.Glass, K.C.

(2024) J Med Chem 67: 8186-8200

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00210
  • Primary Citation of Related Structures:  
    8SDO, 8SDQ, 8SDX, 8UHL, 8UK5

  • PubMed Abstract: 

    The ATPase family AAA + domain containing 2 (ATAD2) protein and its paralog ATAD2B have a C-terminal bromodomain (BRD) that functions as a reader of acetylated lysine residues on histone proteins. Using a structure-function approach, we investigated the ability of the ATAD2/B BRDs to select acetylated lysine among multiple histone post-translational modifications. The ATAD2B BRD can bind acetylated histone ligands that also contain adjacent methylation or phosphorylation marks, while the presence of these modifications significantly weakened the acetyllysine binding activity of the ATAD2 BRD. Our structural studies provide mechanistic insights into how ATAD2/B BRD-binding pocket residues coordinate the acetyllysine group in the context of adjacent post-translational modifications. Furthermore, we investigated how sequence changes in amino acids of the histone ligands impact the recognition of an adjacent acetyllysine residue. Our study highlights how the interplay between multiple combinations of histone modifications influences the reader activity of the ATAD2/B BRDs, resulting in distinct binding modes.

  • Organizational Affiliation

    Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase family AAA domain-containing protein 2B136Homo sapiensMutation(s): 0 
Gene Names: ATAD2BKIAA1240
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULI0 (Homo sapiens)
Explore Q9ULI0 
Go to UniProtKB:  Q9ULI0
GTEx:  ENSG00000119778 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULI0
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, C
14Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on ALY
B, C
Experimental Data & Validation

Experimental Data

  • Resolution: 1.92 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.200 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.119α = 90
b = 55.119β = 90
c = 140.657γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM129338 NIH NIGMS

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release