6VLS | pdb_00006vls

Structure of C-terminal fragment of Vip3A toxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.239 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Insights into the C-terminal Fragment of Insecticidal Vip3A Toxin ofBacillus thuringiensis.

Jiang, K.Zhang, Y.Chen, Z.Wu, D.Cai, J.Gao, X.

(2020) Toxins (Basel) 12

  • DOI: https://doi.org/10.3390/toxins12070438
  • Primary Citation Related Structures: 
    6VLS

  • PubMed Abstract: 

    The vegetative insecticidal proteins (Vips) secreted by Bacillus thuringiensis are regarded as the new generation of insecticidal toxins because they have different insecticidal properties compared with commonly applied insecticidal crystal proteins (Cry toxins). Vip3A toxin, representing the vast majority of Vips, has been used commercially in transgenic crops and bio-insecticides. However, the lack of both structural information on Vip3A and a clear understanding of its insecticidal mechanism at the molecular level limits its further development and broader application. Here we present the first crystal structure of the C-terminal fragment of Vip3A toxin (Vip3Aa11 200-789 ). Since all members of this insecticidal protein family are highly conserved, the structure of Vip3A provides unique insight into the general domain architecture and protein fold of the Vip3A family of insecticidal toxins. Our structural analysis reveals a four-domain organization, featuring a potential membrane insertion region, a receptor binding domain, and two potential glycan binding domains of Vip3A. In addition, cytotoxicity assays and insect bioassays show that the purified C-terminal fragment of Vip3Aa toxin alone have no insecticidal activity. Taken together, these findings provide insights into the mode of action of the Vip3A family of insecticidal toxins and will boost the development of Vip3A into more efficient bio-insecticides.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.

Macromolecule Content 

  • Total Structure Weight: 430.67 kDa 
  • Atom Count: 30,179 
  • Modeled Residue Count: 3,820 
  • Deposited Residue Count: 3,864 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,Vip3Aa
A, B, C, D
966Escherichia coliBacillus thuringiensis
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for W8GI72 (Bacillus thuringiensis)
Explore W8GI72 
Go to UniProtKB:  W8GI72
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9W8GI72
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.239 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.088α = 90
b = 127.884β = 91.38
c = 149.178γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description