4QYL

Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into recognition of acetylated histone ligands by the BRPF1 bromodomain.

Lubula, M.Y.Eckenroth, B.E.Carlson, S.Poplawski, A.Chruszcz, M.Glass, K.C.

(2014) Febs Lett. 588: 3844-3854

  • DOI: 10.1016/j.febslet.2014.09.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bromodomain-PHD finger protein 1 (BRPF1) is part of the MOZ HAT complex and contains a unique combination of domains typically found in chromatin-associated factors, which include plant homeodomain (PHD) fingers, a bromodomain and a proline-tryptopha ...

    Bromodomain-PHD finger protein 1 (BRPF1) is part of the MOZ HAT complex and contains a unique combination of domains typically found in chromatin-associated factors, which include plant homeodomain (PHD) fingers, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. Bromodomains are conserved structural motifs generally known to recognize acetylated histones, and the BRPF1 bromodomain preferentially selects for H2AK5ac, H4K12ac and H3K14ac. We solved the X-ray crystal structures of the BRPF1 bromodomain in complex with the H2AK5ac and H4K12ac histone peptides. Site-directed mutagenesis on residues in the BRPF1 bromodomain-binding pocket was carried out to investigate the contribution of specific amino acids on ligand binding. Our results provide critical insights into the molecular mechanism of ligand binding by the BRPF1 bromodomain, and reveal that ordered water molecules are an essential component driving ligand recognition.


    Organizational Affiliation

    Department of Pharmaceutical Science, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peregrin
A, B, C, D
117Homo sapiensMutation(s): 0 
Gene Names: BRPF1 (BR140)
Find proteins for P55201 (Homo sapiens)
Go to Gene View: BRPF1
Go to UniProtKB:  P55201
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
E, F, G, H
12Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AG, HIST1H2AI, HIST1H2AK, HIST1H2AL, HIST1H2AM (H2AFP, H2AFC, H2AFD, H2AFI, H2AFN)
Find proteins for P0C0S8 (Homo sapiens)
Go to UniProtKB:  P0C0S8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
E, F, G, H
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.908α = 90.00
b = 55.581β = 93.58
c = 82.135γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references
  • Version 1.2: 2014-12-17
    Type: Database references