7M97 | pdb_00007m97

Crystal structure of the bromodomain from Plasmodium falciparum bromodomain protein 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into acetylated histone ligand recognition by the BDP1 bromodomain of Plasmodium falciparum.

Singh, A.K.Phillips, M.Alkrimi, S.Tonelli, M.Boyson, S.P.Malone, K.L.Nix, J.C.Glass, K.C.

(2022) Int J Biol Macromol 223: 316-326

  • DOI: https://doi.org/10.1016/j.ijbiomac.2022.10.247
  • Primary Citation of Related Structures:  
    7M97

  • PubMed Abstract: 

    Plasmodium falciparum requires a two-host system, moving between Anopheles mosquito and humans, to complete its life cycle. To overcome such dynamic growth conditions its histones undergo various post-translational modifications to regulate gene expression. The P. falciparum Bromodomain Protein 1 (PfBDP1) has been shown to interact with acetylated lysine modifications on histone H3 to regulate the expression of invasion-related genes. Here, we investigated the ability of the PfBDP1 bromodomain to interact with acetyllsyine modifications on additional core and variant histones. A crystal structure of the PfBDP1 bromodomain (PfBDP1-BRD) reveals it contains the conserved bromodomain fold, but our comparative analysis between the PfBDP1-BRD and human bromodomain families indicates it has a unique binding mechanism. Solution NMR spectroscopy and ITC binding assays carried out with acetylated histone ligands demonstrate that it preferentially recognizes tetra-acetylated histone H4, and we detected weaker interactions with multi-acetylated H2A.Z in addition to the previously reported interactions with acetylated histone H3. Our findings indicate PfBDP1 may play additional roles in the P. falciparum life cycle, and the distinctive features of its bromodomain binding pocket could be leveraged for the development of new therapeutic agents to help overcome the continuously evolving resistance of P. falciparum against currently available drugs.


  • Organizational Affiliation
    • Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain protein 1131Plasmodium falciparum 3D7Mutation(s): 1 
Gene Names: PF3D7_1033700
UniProt
Find proteins for Q8IJ72 (Plasmodium falciparum (isolate 3D7))
Explore Q8IJ72 
Go to UniProtKB:  Q8IJ72
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IJ72
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.051α = 90
b = 88.667β = 90
c = 106.797γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2021-05-26 
  • Deposition Author(s): Glass, K.C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-27
    Changes: Database references, Structure summary