3LJW

Crystal Structure of the Second Bromodomain of Human Polybromo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.501 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2.

Charlop-Powers, Z.Zeng, L.Zhang, Q.Zhou, M.M.

(2010) Cell Res. 20: 529-538

  • DOI: 10.1038/cr.2010.43
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Polybromo (PB) protein functions as a key component of the human PBAF chromatin remodeling complex in regulation of gene transcription. PB is made up of modular domains including six bromodomains that are known as acetyl-lysine binding domains. H ...

    The Polybromo (PB) protein functions as a key component of the human PBAF chromatin remodeling complex in regulation of gene transcription. PB is made up of modular domains including six bromodomains that are known as acetyl-lysine binding domains. However, histone-binding specificity of the bromodomains of PB has remained elusive. In this study, we report biochemical characterization of all six PB bromodomains' binding to a suite of lysine-acetylated peptides derived from known acetylation sites on human core histones. We demonstrate that bromodomain 2 of PB preferentially recognizes acetylated lysine 14 of histone H3 (H3K14ac), a post-translational mark known for gene transcriptional activation. We further describe the molecular basis of the selective H3K14ac recognition of bromodomain 2 by solving the protein structures in both the free and bound forms using X-ray crystallography and NMR, respectively.


    Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, NY 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein polybromo-1
A, B
120Homo sapiensMutation(s): 0 
Gene Names: PBRM1 (BAF180, PB1)
Find proteins for Q86U86 (Homo sapiens)
Go to Gene View: PBRM1
Go to UniProtKB:  Q86U86
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.501 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 78.964α = 90.00
b = 78.964β = 90.00
c = 50.651γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance