9BCF | pdb_00009bcf

Chimeric protein of crocodile allergen Cro p 1.0101 and GFP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Comparative studies of seafood and reptile alpha- and beta-parvalbumins.

O'Malley, A.Ray, J.M.Kitlas, P.Ruethers, T.Kapingidza, A.B.Cierpicki, T.Lopata, A.Kowal, K.Chruszcz, M.

(2024) Protein Sci 33: e5226-e5226

  • DOI: https://doi.org/10.1002/pro.5226
  • Primary Citation of Related Structures:  
    9B26, 9BAR, 9BB8, 9BCF

  • PubMed Abstract: 

    Small calcium-binding proteins such as parvalbumins (PVs) are major seafood and fish allergens. However, the impact of structural changes on their capacity to bind IgE has not been studied in detail. Therefore, fish and reptilian PVs, as well as human α-PV, were selected for biochemical, structural, and IgE binding studies. Likely due to their high solubility, crystallization proved difficult, so additional techniques were used to promote crystallization of the proteins. Novel crystal structures were determined for human PV, cod allergen Gad m 1.0201, saltwater crocodile allergen Cro p 1.0101, and the α-PV from thornback ray. β-PVs are considered the major fish allergens, while α-PVs are rarely categorized as allergens. To explain these differences, the results of structural and IgE binding studies were combined. This approach allowed us to provide new insight into IgE binding epitopes present on PVs, focusing on cross-reactivity among the selected α- and β-PVs. In addition, we have shown that these proteins display remarkable thermal stability across a range of pH conditions, which is relevant in the case of food allergens and food processing. Moreover, it is shown that the presence of calcium cations is critical for stability of the studied PVs via their protein folding, which has an impact on the formation of IgE binding epitopes. These studies shows the stability of fish and reptile PV allergens, and it allows for further evaluation of their IgE cross-reactivity.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Parvalbumin, Green fluorescent protein chimera
A, B, C
358Crocodylus porosusAequorea victoria
This entity is chimeric
Mutation(s): 1 
Gene Names: LOC109314825gfp
UniProt
Find proteins for A0A7M4EAX1 (Crocodylus porosus)
Explore A0A7M4EAX1 
Go to UniProtKB:  A0A7M4EAX1
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212A0A7M4EAX1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRO
Query on CRO
A, B, C
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.778α = 90
b = 158.778β = 90
c = 123.498γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references