8ZS0 | pdb_00008zs0

Plasmodium falciparum Nucleoplasmin (PfNPM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 
    0.263 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-function studies of a nucleoplasmin isoform from Plasmodium falciparum.

Saharan, K.Baral, S.Gandhi, S.Singh, A.K.Ghosh, S.Das, R.Nagaraj, V.A.Vasudevan, D.

(2025) J Biological Chem 301: 108379-108379

  • DOI: https://doi.org/10.1016/j.jbc.2025.108379
  • Primary Citation of Related Structures:  
    8ZS0

  • PubMed Abstract: 

    An organized regulation of gene expression and DNA replication is vital for the progression of the complex life cycle of Plasmodium falciparum (Pf), involving multiple hosts and various stages. These attributes rely on the dynamic architecture of chromatin governed by several factors, including histone chaperones. Nucleoplasmin class of histone chaperones perform histone chaperoning function and participate in various developmental processes in eukaryotes. Here, our crystal structure confirmed that Pf indeed possesses a nucleoplasmin isoform (PfNPM), and the N-terminal core domain (NTD) adopts the characteristic pentameric doughnut conformation. Furthermore, PfNPM exists as a pentamer in solution, and the N-terminal core domain exhibits thermal and chemical stability. PfNPM interacts individually with assembled H2A/H2B and H3/H4 with an equimolar stoichiometry, wherein the acidic tracts of PfNPM were found to be necessary for these interactions. Further, H3/H4 displays a higher binding affinity for PfNPM than H2A/H2B, potentially due to stronger electrostatic interactions. The interaction studies also suggested that H2A/H2B and H3/H4 might share the same binding site on the PfNPM distal face, wherein H3/H4 could substitute H2A/H2B due to a higher binding affinity. Intriguingly, PfNPM neither demonstrated direct interaction with the nucleosome core particles nor displayed nucleosome assembly function, suggesting it may not be directly associated with histone deposition on the parasite genomic DNA. Furthermore, our immunofluorescence results suggested that PfNPM predominantly localizes in the nucleus and exhibits expression only in the early blood stages, such as ring and trophozoite. Altogether, we provide the first report on the structural and functional characterization of PfNPM.


  • Organizational Affiliation
    • Structural Biology Laboratory, BRIC-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India; Regional Centre for Biotechnology, Faridabad, India.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoplasmin-like domain-containing proteinA [auth B],
B [auth A],
C,
D,
E
107Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0813300
UniProt
Find proteins for C0H4U4 (Plasmodium falciparum (isolate 3D7))
Explore C0H4U4 
Go to UniProtKB:  C0H4U4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0H4U4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free:  0.263 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.349α = 90
b = 89.349β = 90
c = 113.282γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/INF/22/SP22660/2017
Department of Biotechnology (DBT, India)IndiaBT/INF/22/SP33046/2019
Science and Engineering Research Board (SERB)IndiaCRG/2023/002836

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release