9FDO | pdb_00009fdo

Structure of synthetic C-terminal biotinylated schistosomin with the point mutation D88E from Biomphalaria glabrata in C2 space group

PDB DOI: https://doi.org/10.2210/pdb9FDO/pdb

Classification: TOXIN
Organism(s): Biomphalaria glabrata
Mutation(s): Yes

Deposited: 2024-05-17 Released: 2025-05-28
Deposition Author(s): Morera, S., Vigouroux, A., Legrand, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.275 (Depositor), 0.265 (DCC)
R-Value Work:
0.229 (Depositor), 0.221 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Total synthesis and structural characterization of a novel protein scaffold from the snail Biomphalaria glabrata.

Melnyk, O., Caby, S., Vigouroux, A., Demanche, C., Desmet, R., Senechal, M., Snella, B., Mougel, A., Boidin-Wichlacz, C., Parmentier, A., Pasco, U., Cantel, S., Morera, S., Vicogne, J.

(2026) Protein Sci 35: e70745-e70745

PubMed: 42554520 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70745
Primary Citation Related Structures:
9FDO, 9RT6

PubMed Abstract:
Disulfide-rich miniproteins constitute compact and highly stable scaffolds of growing interest for molecular and structural engineering. Schistosomins are ~80-residue proteins conserved across gastropods that form a long-standing orphan family whose structure and biological roles have remained unknown. Here, we report the total chemical synthesis and structural characterization of a schistosomin isoform from Biomphalaria glabrata, a medically relevant intermediate host of the parasite Schistosoma mansoni. Using state-of-the-art solid-phase peptide synthesis, chemoselective peptide ligation, and controlled oxidative folding, we obtained homogeneous, well-folded schistosomin suitable for biophysical and structural studies. High-resolution X-ray crystallography reveals a previously undescribed disulfide-rich fold defining a new class of miniprotein scaffold. Nano differential scanning fluorimetry and circular dichroism experiments demonstrate the remarkable thermal stability of this scaffold. Complementary in silico analyses suggest that the two naturally occurring isoforms, which differ by a single residue, exhibit highly similar structural and dynamic properties. Finally, transcript and protein analyses across snail tissues provide the first spatial expression map of schistosomin in a medically relevant mollusk. Together, this work establishes schistosomin as a novel and robust miniprotein scaffold and provides a structural and biological framework for exploring its function and potential applications.

Organizational Affiliation

Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France.

Macromolecule Content

Total Structure Weight: 18.66 kDa
Atom Count: 1,348
Modeled Residue Count: 158
Deposited Residue Count: 160
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Schistosomin	A, B	80	Biomphalaria glabrata	Mutation(s): 1
UniProt
Find proteins for B5L013 (Biomphalaria glabrata) Explore B5L013 Go to UniProtKB: B5L013
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5L013
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTN Query on BTN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.275 (Depositor), 0.265 (DCC)
R-Value Work: 0.229 (Depositor), 0.221 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.68	α = 90
b = 37.96	β = 95.35
c = 43.19	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
autoPROC	data processing
autoPROC	data processing
XSCALE	data scaling
BUSTER	refinement
autoPROC	data reduction
PHASER	phasing
STARANISO	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-28

Deposition Author(s):

Morera, S.

Vigouroux, A.

Legrand, P.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-28
Type: Initial release
Version 1.1: 2025-12-10
Changes: Data collection, Database references, Refinement description, Source and taxonomy, Structure summary
Version 1.2: 2026-09-09
Changes: Database references