9IID | pdb_00009iid

Crystal structure of PgAfp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.174 (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

The role of Npt1 in regulating antifungal protein activity in filamentous fungi.

Wang, Y.Wang, S.Chen, Y.Xie, C.Xu, H.Lin, Y.Lin, R.Zeng, W.Chen, X.Nie, X.Wang, S.

(2025) Nat Commun 16: 2850-2850

  • DOI: https://doi.org/10.1038/s41467-025-58230-6
  • Primary Citation of Related Structures:  
    9IID

  • PubMed Abstract: 

    Pathogenic filamentous fungi pose a significant threat to global food security and human health. The limitations of available antifungal agents, including resistance and toxicity, highlight the need for developing innovative antifungal strategies. Antifungal proteins (AFPs) are a class of secreted small proteins that exhibit potent antifungal activity against filamentous fungi, yet the underlying mechanism remains partially understood. In this study, we investigate the molecular and cellular effects of two AFPs, PgAFP and AfAFP, on Aspergillus flavus, a representative filamentous fungus. These AFPs affect various fungal phenotypes and exert an intracellular effect by interacting with Ntp1, a fungi exclusive protein modulating diverse fungal traits. We find that Ntp1 amino acids 417-588 are critical for AFP binding and play a role in regulating growth, development, sporulation, sclerotia formation, toxin synthesis, and pathogenicity. Results generated from this study will help to control pathogenic fungi.


  • Organizational Affiliation
    • The State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antifungal protein B60Penicillium chrysogenumMutation(s): 0 
Gene Names: pafB
UniProt
Find proteins for D0EXD3 (Penicillium chrysogenum)
Explore D0EXD3 
Go to UniProtKB:  D0EXD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0EXD3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.76α = 90
b = 61.76β = 90
c = 42γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-07-10 
  • Deposition Author(s): Wang, Y.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary
  • Version 1.2: 2025-05-21
    Changes: Database references