triosephosphate isomerase-scylla paramamosain

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Crystal Structure Analysis and Conformational Epitope Mutation of Triosephosphate Isomerase, a Mud Crab Allergen.

Xia, F.Li, M.S.Liu, Q.M.Liu, M.Yang, Y.Cao, M.J.Chen, G.X.Jin, T.Liu, G.M.

(2019) J Agric Food Chem 67: 12918-12926

  • DOI: https://doi.org/10.1021/acs.jafc.9b05279
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The triosephosphate isomerase (TIM), Scy p 8, is a crab allergen and shows cross-reactivity in the shellfish. Here, recombinant Scy p 8 was expressed, and its crystal structure was determined at a resolution of 1.8 Å. The three-dimensional structure of Scy p 8 is primarily composed of a (β/α) 8 -barrel motif prototype. Additionally, Scy p 8 showed cross-reactivity with high sequential and secondary structural identity among TIMs from shellfish species. The site-directed mutagenesis of critical amino acids of conformational epitopes was carried out, and the mutants of Trp 168 and Lys 237 to Ala reduced immunoglobulin E (IgE)-binding activity by approximately 30%, compared with wild-type TIM in an inhibition ELISA; however, it still induced basophil activation despite the interpatient variability between patients. These results can help to provide an accurate template for the analysis of the IgE binding and establish meaningful relationships between structure and allergenicity.

  • Organizational Affiliation

    College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources , Jimei University , Xiamen , Fujian 361021 , China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Triosephosphate isomeraseA [auth B],
B [auth A]
269Scylla paramamosainMutation(s): 0 
Find proteins for A0A1L5YRA2 (Scylla paramamosain)
Explore A0A1L5YRA2 
Go to UniProtKB:  A0A1L5YRA2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L5YRA2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.712α = 90
b = 154.712β = 90
c = 52.713γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description