6VEO | pdb_00006veo

ATAD2B bromodomain in complex with 4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl]amino}piperidin-3-yl]oxy}methyl)-1lambda~6~-thiane-1,1-dione (compound 38)

• PDB DOI: https://doi.org/10.2210/pdb6VEO/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-02 Released: 2020-10-28 
• Deposition Author(s): Glass, K.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into the Recognition of Mono- and Diacetylated Histones by the ATAD2B Bromodomain.

Lloyd, J.T., McLaughlin, K., Lubula, M.Y., Gay, J.C., Dest, A., Gao, C., Phillips, M., Tonelli, M., Cornilescu, G., Marunde, M.R., Evans, C.M., Boyson, S.P., Carlson, S., Keogh, M.C., Markley, J.L., Frietze, S., Glass, K.C.

(2020) J Med Chem 63: 12799-12813

• PubMed: 33084328 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c01178
• Primary Citation Related Structures: 
  6VEO


• PubMed Abstract: 
  

  Bromodomains exhibit preferences for specific patterns of post-translational modifications on core and variant histone proteins. We examined the ligand specificity of the ATAD2B bromodomain and compared it to its closely related paralogue in ATAD2. We show that the ATAD2B bromodomain recognizes mono- and diacetyllysine modifications on histones H4 and H2A. A structure-function approach was used to identify key residues in the acetyllysine-binding pocket that dictate the molecular recognition process, and we examined the binding of an ATAD2 bromodomain inhibitor by ATAD2B. Our analysis demonstrated that critical contacts required for bromodomain inhibitor coordination are conserved between the ATAD2/B bromodomains, with many residues playing a dual role in acetyllysine recognition. We further characterized an alternative splice variant of ATAD2B that results in a loss of function. Our results outline the structural and functional features of the ATAD2B bromodomain and identify a novel mechanism regulating the interaction of the ATAD2B protein with chromatin.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States.
Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States.
National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
EpiCypher Inc., Durham, North Carolina 27709, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 16.53 kDa 
• Atom Count: 1,284 
• Modeled Residue Count: 136 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family AAA domain-containing protein 2B	A	136	Homo sapiens	Mutation(s): 0  Gene Names: ATAD2B, KIAA1240
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULI0 (Homo sapiens) Explore Q9ULI0  Go to UniProtKB:  Q9ULI0
PHAROS:  Q9ULI0 GTEx:  ENSG00000119778

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YD4 (Subject of Investigation/LOI)	D [auth A]	4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl]amino}piperidin-3-yl]oxy}methyl)-1lambda~6~-thiane-1,1-dione C26 H33 N5 O4 S ZIRMKCLZUOCUSC-DHIUTWEWSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.358	α = 90
b = 76.358	β = 90
c = 102.312	γ = 120

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
PROTEUM	data reduction
PROTEUM	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): Glass, K.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM129338
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R15GM104865

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2020-11-25
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description