5NNF

Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated BAZ1B peptide (K221ac)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains.

Lambert, J.P.Picaud, S.Fujisawa, T.Hou, H.Savitsky, P.Uuskula-Reimand, L.Gupta, G.D.Abdouni, H.Lin, Z.Y.Tucholska, M.Knight, J.D.R.Gonzalez-Badillo, B.St-Denis, N.Newman, J.A.Stucki, M.Pelletier, L.Bandeira, N.Wilson, M.D.Filippakopoulos, P.Gingras, A.C.

(2019) Mol. Cell 73: 621-638.e17

  • DOI: 10.1016/j.molcel.2018.11.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Targeting bromodomains (BRDs) of the bromo-and-extra-terminal (BET) family offers opportunities for therapeutic intervention in cancer and other diseases. Here, we profile the interactomes of BRD2, BRD3, BRD4, and BRDT following treatment with the pa ...

    Targeting bromodomains (BRDs) of the bromo-and-extra-terminal (BET) family offers opportunities for therapeutic intervention in cancer and other diseases. Here, we profile the interactomes of BRD2, BRD3, BRD4, and BRDT following treatment with the pan-BET BRD inhibitor JQ1, revealing broad rewiring of the interaction landscape, with three distinct classes of behavior for the 603 unique interactors identified. A group of proteins associate in a JQ1-sensitive manner with BET BRDs through canonical and new binding modes, while two classes of extra-terminal (ET)-domain binding motifs mediate acetylation-independent interactions. Last, we identify an unexpected increase in several interactions following JQ1 treatment that define negative functions for BRD3 in the regulation of rRNA synthesis and potentially RNAPII-dependent gene expression that result in decreased cell proliferation. Together, our data highlight the contributions of BET protein modules to their interactomes allowing for a better understanding of pharmacological rewiring in response to JQ1.


    Organizational Affiliation

    Department of Gynecology, University of Zurich, Wagistrasse 14, 8952 Schlieren, Switzerland.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada.,Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK. Electronic address: panagis.filippakopoulos@sgc.ox.ac.uk.,Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.,Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada; Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, ON, Canada.,Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada; Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia.,Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. Electronic address: gingras@lunenfeld.ca.,Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A
127Homo sapiensMutation(s): 0 
Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens)
Go to Gene View: BRD4
Go to UniProtKB:  O60885
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FLPH(ALY)YDVKL
B
10Homo sapiensMutation(s): 0 
Gene Names: BAZ1B (WBSC10, WBSCR10, WBSCR9, WSTF)
EC: 2.7.10.2
Find proteins for Q9UIG0 (Homo sapiens)
Go to Gene View: BAZ1B
Go to UniProtKB:  Q9UIG0
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.119 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.439α = 90.00
b = 43.915β = 90.00
c = 79.690γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
XDSdata reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-11-28
    Type: Data collection, Database references
  • Version 1.2: 2018-12-26
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Data collection, Database references