Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
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: 15939.34 
• Atom Count: 1031 
• Residue Count: 132 
• Unique protein chains: 2

5GH9

Crystal structure of CBP Bromodomain with H3K56ac peptide

• DOI: 10.2210/pdb5GH9/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG'


• Deposited: 2016-06-19 Released: 2017-06-21 
• Deposition Author(s): Xu, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.451 Å
• R-Value Free: 0.176 
• R-Value Work: 0.145 

Literature

Structural insight into CBP bromodomain-mediated recognition of acetylated histone H3K56ac

Xu, L., Cheng, A., Huang, M., Zhang, J., Jiang, Y., Wang, C., Li, F., Bao, H., Gao, J., Wang, N., Liu, J., Wu, J., Wong, C.C.L., Ruan, K.

(2017) FEBS J. --: --

• PubMed: 28815970 
• DOI: 10.1111/febs.14198


• PubMed Abstract: 
  

The acetylation of lysine 56 of histone H3 (H3K56ac) enhances the binding affinity of histone chaperones to H3-H4 dimers. CREB-binding protein (CBP) possesses a bromodomain that recognizes H3K56 acetylation. CBP also possesses a histone acetyltransferase (HAT) domain, which has been shown to promote H3K56 acetylation of free histones to facilitate delivery of replication-dependent chaperones to acetylated histones for chromatin assembly. However, the mechanism by which the CBP bromodomain recognizes H3K56ac and the context in which such recognition occurs remain elusive. Here, we solved the crystal structure of the CBP bromodomain in complex with an H3K56ac peptide. Our data demonstrate that the CBP bromodomain recognizes H3K56ac with high affinity. Structural and affinity analyses reveal that the CBP bromodomain prefers an aromatic residue at the -2 position and an arginine at the -4 position from the acetyl-lysine, and that the CBP bromodomain selectively recognizes an extended conformation of the H3 αN helix that contains H3K56ac. We also demonstrate that the CBP bromodomain binds to H3K56ac in a recombinant H3-H4 dimer but not in a mono-nucleosome. Our results suggest that the CBP bromodomain selectively recognizes an extended conformation of the K56-acetylated H3 α _N region within an H3-H4 dimer, which is expected to facilitate the HAT activity of CBP for subsequent H3K56 acetylation of free histones.

---

Organizational Affiliation: 

National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CREB-binding protein	A	118	Homo sapiens	Mutation(s): 0  Gene Names: CREBBP (CBP) EC: 2.3.1.48
Find proteins for Q92793 (Homo sapiens) Go to Gene View: CREBBP Go to UniProtKB:  Q92793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H3	B	14	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens) Go to Gene View: HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J Go to UniProtKB:  P68431

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: 1.451 Å
• R-Value Free: 0.176 
• R-Value Work: 0.145 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 42.826	α = 90.00
b = 45.832	β = 90.00
c = 66.038	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-06-19 
• Released Date: 2017-06-21 
• Deposition Author(s): Xu, L.

Revision History 

• Version 1.0: 2017-06-21
  Type: Initial release
• Version 1.1: 2017-08-30
  Type: Database references