9W4X | pdb_00009w4x

N-terminal half domain of EPC3


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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Literature

Identification and NMR-based structural characterization of the functional domain of EPC3, a virulence effector of the phytopathogenic fungus Colletotrichum orbiculare.

Xu, Z.Singkaravanit-Ogawa, S.Takano, Y.Ohki, S.

(2025) Front Plant Sci 16: 1691993-1691993

  • DOI: https://doi.org/10.3389/fpls.2025.1691993
  • Primary Citation Related Structures: 
    9W4X

  • PubMed Abstract: 

    Plant pathogens secrete various effector proteins to induce infections in their host plants. Understanding the molecular basis of plant pathogen effectors is important for improving agricultural productivity, plant health, and sustainability. However, this remains a significant challenge. EPC3 (EPC; Effector Protein for Cucurbit infection) is a recently discovered effector involved in the virulence of the cucurbit anthracnose fungus Colletotrichum orbiculare on host plants, although the structure-function relationship is unknown. Here, we report that the N-terminal half domain of EPC3 is responsible for its function. We determined the solution nuclear magnetic resonance (NMR) structure and dynamic properties of this functional domain. The structure containing three disulfide (SS) bonds is composed of five β-strands. The molecule was rigid except for the loop regions connecting β-strands. The structural properties were compared with those of other structurally similar effectors to deduce the potential residues responsible for this function. Furthermore, mutation experiments demonstrated the importance of intramolecular disulfide bonds in maintaining the structural integrity of EPC3. Our results provided insights into the molecular characteristics of EPC3 and a basis for future structure-guided functional studies.


  • Organizational Affiliation
    • Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology (JAIST), Nomi, Japan.

Macromolecule Content 

  • Total Structure Weight: 7.78 kDa 
  • Atom Count: 541 
  • Modeled Residue Count: 68 
  • Deposited Residue Count: 68 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
EPC368Colletotrichum orbiculareMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20K06049
Japan Society for the Promotion of Science (JSPS)Japan21H050032
Japan Society for the Promotion of Science (JSPS)Japan25H00431

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release