Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 16.58 kDa 
• Atom Count: 1076 
• Residue Count: 119 
• 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)
• Mutation(s): No 


• 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 
• R-Value Observed: 0.186 

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:  
  2RFJ, 2NXB, 2OO1, 2OSS, 2OUO, 3MQM, 3LXJ, 3NXB, 3UVW, 3UVX


• 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B	11	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805 GTEx  ENSG00000274618GTEx  ENSG00000197238GTEx  ENSG00000197837GTEx  ENSG00000158406GTEx  ENSG00000278705GTEx  ENSG00000197061GTEx  ENSG00000270882GTEx  ENSG00000270276GTEx  ENSG00000273542GTEx  ENSG00000277157GTEx  ENSG00000276966GTEx  ENSG00000276180GTEx  ENSG00000278637GTEx  ENSG00000275126

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885 GTEx  ENSG00000141867

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 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.225	α = 90
b = 50.478	β = 90
c = 51.969	γ = 90

Software Package:

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

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
  Changes: Database references