6SSV | pdb_00006ssv

The structure of serpin from Schistosoma mansoni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 
    0.231 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6SSV

This is version 1.3 of the entry. See complete history

Literature

Structure, Immunoreactivity, and In Silico Epitope Determination of SmSPI S. mansoni Serpin for Immunodiagnostic Application.

De Benedetti, S.Di Pisa, F.Fassi, E.M.A.Cretich, M.Musico, A.Frigerio, R.Mussida, A.Bombaci, M.Grifantini, R.Colombo, G.Bolognesi, M.Grande, R.Zanchetta, N.Gismondo, M.R.Mileto, D.Mancon, A.Gourlay, L.J.

(2021) Vaccines (Basel) 9

  • DOI: https://doi.org/10.3390/vaccines9040322
  • Primary Citation Related Structures: 
    6SSV

  • PubMed Abstract: 

    The human parasitic disease Schistosomiasis is caused by the Schistosoma trematode flatworm that infects freshwaters in tropical regions of the world, particularly in Sub-Saharan Africa, South America, and the Far-East. It has also been observed as an emerging disease in Europe, due to increased immigration. In addition to improved therapeutic strategies, it is imperative to develop novel, rapid, and sensitive diagnostic tests that can detect the Schistosoma parasite, allowing timely treatment. Present diagnosis is difficult and involves microscopy-based detection of Schistosoma eggs in the feces. In this context, we present the 3.22 Å resolution crystal structure of the circulating antigen Serine protease inhibitor from S. mansoni (SmSPI), and we describe it as a potential serodiagnostic marker. Moreover, we identify three potential immunoreactive epitopes using in silico-based epitope mapping methods. Here, we confirm effective immune sera reactivity of the recombinant antigen, suggesting the further investigation of the protein and/or its predicted epitopes as serodiagnostic Schistosomiasis biomarkers.


  • Organizational Affiliation
    • Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.

Macromolecule Content 

  • Total Structure Weight: 43.94 kDa 
  • Atom Count: 2,690 
  • Modeled Residue Count: 365 
  • Deposited Residue Count: 388 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serpin, putative388Schistosoma mansoniMutation(s): 0 
Gene Names: Smp_090080
UniProt
Find proteins for G4LYU6 (Schistosoma mansoni)
Explore G4LYU6 
Go to UniProtKB:  G4LYU6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4LYU6
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free:  0.231 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.887α = 90
b = 98.887β = 90
c = 115.338γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
pointlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2021-05-12
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description