5GH9

Crystal structure of CBP Bromodomain with H3K56ac peptide


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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. --: --

  • 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 acetyltransfe ...

    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
MoleculeChainsSequence LengthOrganismDetails
CREB-binding protein
A
118Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
Histone H3
B
14Homo sapiensMutation(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 UniProtKB:  P68431
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: 1.451 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.826α = 90.00
b = 45.832β = 90.00
c = 66.038γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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