Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16332.76 
• Atom Count: 1095 
• Residue Count: 139 
• Unique protein chains: 2

3JVK

Crystal structure of bromodomain 1 of mouse Brd4 in complex with histone H3-K(ac)14

• DOI: 10.2210/pdb3JVK/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli


• Deposited: 2009-09-17 Released: 2009-10-13 
• Deposition Author(s): Blankenfeldt, W., Geyer, M., Vollmuth, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.259 
• R-Value Work: 0.196 

Literature

Structures of the Dual Bromodomains of the P-TEFb-activating Protein Brd4 at Atomic Resolution

Vollmuth, F., Blankenfeldt, W., Geyer, M.

(2009) J.Biol.Chem. 284: 36547-36556

• PubMed: 19828451 
• DOI: 10.1074/jbc.M109.033712
• Primary Citation of Related Structures:  
  3JVM, 3JVL, 3JVJ


• PubMed Abstract: 
  

Brd4 is a member of the bromodomains and extra terminal domain (BET) family of proteins that recognize acetylated chromatin structures through their bromodomains and act as transcriptional activators. Brd4 functions as an associated factor and positive regulator of P-TEFb, a Cdk9-cyclin T heterodimer that stimulates transcriptional elongation by RNA polymerase II. Here, the crystal structures of the two bromodomains of Brd4 (BD1 and BD2) were determined at 1.5 and 1.2 A resolution, respectively. Complex formation of BD1 with a histone H3 tail polypeptide encompassing residues 12-19 showed binding of the Nzeta-acetylated lysine 14 to the conserved asparagine 140 of Brd4. In contrast, in BD2 the N-terminal linker sequence was found to interact with the binding site for acetylated lysines of the adjacent molecule to form continuous strings in the crystal lattice. This assembly shows for the first time a different binding ligand than acetylated lysine indicating that also other sequence compositions may be able to form similar interaction networks. Isothermal titration calorimetry revealed best binding of BD1 to H3 and of BD2 to H4 acetylated lysine sequences, suggesting alternating histone recognition specificities. Intriguingly, an acetylated lysine motif from cyclin T1 bound similarly well to BD2. Whereas the structure of Brd2 BD1 suggested its dimer formation, both Brd4 bromodomains appeared monomeric in solution as shown by size exclusion chromatography and mutational analyses.

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Organizational Affiliation: 

Abteilung Physikalische Biochemie, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Bromodomain-containing protein 4	A	131	Mus musculus	Mutation(s): 0  Gene Names: Brd4 (Mcap)
Find proteins for Q9ESU6 (Mus musculus) Go to UniProtKB:  Q9ESU6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
histone H3.3 peptide	C	8	Homo sapiens	Mutation(s): 0  Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens) Go to Gene View: H3F3A H3F3B Go to UniProtKB:  P84243

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.259 
• R-Value Work: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 36.131	α = 90.00
b = 47.030	β = 90.00
c = 77.250	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
ADSC	data collection
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-17 
• Released Date: 2009-10-13 
• Deposition Author(s): Blankenfeldt, W., Geyer, M., Vollmuth, F.

Revision History 

• Version 1.0: 2009-10-13
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance