Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 16580.10 
• Atom Count: 1011 
• Residue Count: 138 
• Unique protein chains: 2

3UVY

Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K16acK20ac)

• DOI: 10.2210/pdb3UVY/pdb

• Classification: TRANSCRIPTION/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2011-11-30 Released: 2012-01-18 
• Deposition Author(s): Filippakopoulos, P., Felletar, I., Picaud, S., Keates, T., Muniz, J., Gileadi, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.258 
• R-Value Work: 0.181 

Literature

Histone recognition and large-scale structural analysis of the human bromodomain family.

Filippakopoulos, P., Picaud, S., Mangos, M., Keates, T., Lambert, J.P., Barsyte-Lovejoy, D., Felletar, I., Volkmer, R., Muller, S., Pawson, T., Gingras, A.C., Arrowsmith, C.H., Knapp, S.

(2012) Cell 149: 214-231

• PubMed: 22464331 
• DOI: 10.1016/j.cell.2012.02.013
• Primary Citation of Related Structures:  
  3UVX, 3UV4, 3UV2, 3RCW, 3P1D, 3P1C, 3NXB, 3LXJ, 3GG3, 3DWY, 3DAI, 3UW9, 3UVW, 3UVD, 3UV5, 3TLP, 3Q2E, 3MQM, 3MB4, 3MB3, 3IU6, 3IU5, 3I3J, 3HMH, 3HMF, 3HME, 3D7C, 2RFJ, 2OUO, 2OSS, 2OO1, 2NXB


• PubMed Abstract: 
  

Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resolution crystal structures, covering all BRD families. Comprehensive crossfamily structural analysis identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-containing peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.

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Organizational Affiliation: 

Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens) Go to Gene View: BRD4 Go to UniProtKB:  O60885

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B	11	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens) Go to Gene View: HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4 Go to UniProtKB:  P62805

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.258 
• R-Value Work: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 43.225	α = 90.00
b = 50.478	β = 90.00
c = 51.969	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
PDB_EXTRACT	data extraction
SCALA	data scaling
XDS	data reduction
GDA	data collection
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-30 
• Released Date: 2012-01-18 
• Deposition Author(s): Filippakopoulos, P., Felletar, I., Picaud, S., Keates, T., Muniz, J., Gileadi, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History 

• Version 1.0: 2012-01-18
  Type: Initial release
• Version 1.1: 2012-04-11
  Type: Database references