9J9W | pdb_00009j9w

A broad-spectrum anti-fungal effector dictates bacterial-fungal interkingdom interactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.285 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9J9W

This is version 1.1 of the entry. See complete history

Literature

A broad-spectrum anti-fungal effector dictates bacterial-fungal interkingdom interactions.

Yan, S.Zou, Y.Wu, T.Kan, Y.Luo, H.Pei, T.T.Liang, X.An, Y.Meng, P.Song, Y.Qin, W.M.Chen, C.Dong, T.

(2025) PLoS Pathog 21: e1013598-e1013598

  • DOI: https://doi.org/10.1371/journal.ppat.1013598
  • Primary Citation Related Structures: 
    9J9W

  • PubMed Abstract: 

    Bacteria-fungi interactions play crucial roles in shaping microbial communities across diverse environmental and host-associated niches. While their antagonism through diffusible metabolites is a well-known ecological phenomenon, delivery of bacterial effectors into the nucleus of fungal cells remains rare, and the mechanisms are poorly understood. Here, we identify and characterize a potent anti-fungal nuclease effector, TseN, delivered by the type VI secretion system (T6SS) of Acidovorax citrulli. TseN possesses a nuclear localization signal and inhibits multiple fungal species, including emerging human pathogens Candida auris and Cryptococcus neoformans. Structural and biochemical analyses show that TseN possesses a unique C-terminal DNase domain that defines a new effector class, with its activity neutralized by a cognate immunity protein TsiN. The delivery of TseN requires the upstream-encoded VgrG5, a chaperone Aave_2128, and PAAR5. Transcriptome profiling of co-cultured bacterial-fungal cells demonstrates that the T6SS attack triggers extensive reprogramming in fungal cells, affecting DNA repair, stress response, and filamentation pathways. These responses not only compromise fungal survival but also modulate fungal drug resistance, as evidenced by the synergistic enhancement of azole efficacy against drug-resistant Candida albicans. Importantly, in vivo experiments confirm that the T6SS, via TseN, can significantly reduce fungal burden on murine skin. Phylogenetic analysis shows TseN homologs are present in a large number of bacterial species. Collectively, our findings highlight a previously underappreciated interkingdom antagonism modulated by a novel effector. The broad-spectrum anti-fungal activities of TseN and its homologs may be explored for therapeutic strategies targeting fungal pathogens in both clinical and environmental settings.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 34.94 kDa 
  • Atom Count: 2,424 
  • Modeled Residue Count: 310 
  • Deposited Residue Count: 314 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TsiN158Paracidovorax citrulli AAC00-1Mutation(s): 0 
Gene Names: Aave_2131
UniProt
Find proteins for A1TP23 (Paracidovorax citrulli (strain AAC00-1))
Explore A1TP23 
Go to UniProtKB:  A1TP23
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1TP23
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TseN156Paracidovorax citrulli AAC00-1Mutation(s): 0 
Gene Names: Aave_2130
UniProt
Find proteins for A1TP22 (Paracidovorax citrulli (strain AAC00-1))
Explore A1TP22 
Go to UniProtKB:  A1TP22
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1TP22
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.285 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.93α = 90
b = 86.93β = 90
c = 170.662γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2020YFA0907200

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2026-05-06
    Changes: Database references