9FEI | pdb_00009fei

Crystal structure of protein D: defoliating toxin form Fusarium oxysporum f.sp. vasinfectum

PDB DOI: https://doi.org/10.2210/pdb9FEI/pdb

Classification: TOXIN
Organism(s): Fusarium oxysporum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-20 Released: 2025-05-28
Deposition Author(s): Troilo, F., Doddi, A., Faino, L., Bonaccorsi Di Patti, M.C., Di Matteo, A., Giardina, G.
Funding Organization(s): Other government, European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.188 (Depositor), 0.205 (DCC)
R-Value Work:
0.161 (Depositor)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9FEI

This is version 1.1 of the entry. See complete history.

Literature

A structurally unique effector shared between vascular wilt fungi drives cotton and olive defoliation

Doddi, A., Fiorin, G.L., Li, J., Zannini, I., Sato, Y., Lancia, G., Giuliari, G., Gomez-Lama Cabanas, C., Valverde-Corredor, A., Liu, T., Tian, H., van den Berg, G.C.M., Mercado-Blanco, J., Zhang, B., Seidl, M.F., Rep, M., Groot, W., Bonaccorsi Di Patti, M.C., Troilo, F., Di Matteo, A., Giardina, G., Reverberi, M., Zhu, L., Faino, L., Thomma, B.P.H.J.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-74504-z

Macromolecule Content

Total Structure Weight: 27.52 kDa
Atom Count: 1,680
Modeled Residue Count: 185
Deposited Residue Count: 239
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Defoliating protein: protein D	A	239	Fusarium oxysporum	Mutation(s): 0
UniProt
Find proteins for A0A2H3FS34 (Fusarium oxysporum f. sp. radicis-cucumerinum) Explore A0A2H3FS34 Go to UniProtKB: A0A2H3FS34
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2H3FS34
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
HG Query on HG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.188 (Depositor), 0.205 (DCC)
R-Value Work: 0.161 (Depositor)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.843	α = 90
b = 50.031	β = 98.91
c = 72.277	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
CRANK2	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-28

Deposition Author(s):

Bonaccorsi Di Patti, M.C.

Funding Organization	Location	Grant Number
Other government		RM12117A5BDD4AEC
European Union (EU)	European Union	IR0000009

Revision History (Full details and data files)

Version 1.0: 2025-05-28
Type: Initial release
Version 1.1: 2026-07-01
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.