6TFK

Vip3Aa toxin structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular architecture and activation of the insecticidal protein Vip3Aa from Bacillus thuringiensis.

Nunez-Ramirez, R.Huesa, J.Bel, Y.Ferre, J.Casino, P.Arias-Palomo, E.

(2020) Nat Commun 11: 3974-3974

  • DOI: https://doi.org/10.1038/s41467-020-17758-5
  • Primary Citation of Related Structures:  
    6TFJ, 6TFK

  • PubMed Abstract: 

    Bacillus thuringiensis Vip3 (Vegetative Insecticidal Protein 3) toxins are widely used in biotech crops to control Lepidopteran pests. These proteins are produced as inactive protoxins that need to be activated by midgut proteases to trigger cell death. However, little is known about their three-dimensional organization and activation mechanism at the molecular level. Here, we have determined the structures of the protoxin and the protease-activated state of Vip3Aa at 2.9 Å using cryo-electron microscopy. The reconstructions show that the protoxin assembles into a pyramid-shaped tetramer with the C-terminal domains exposed to the solvent and the N-terminal region folded into a spring-loaded apex that, after protease activation, drastically remodels into an extended needle by a mechanism akin to that of influenza haemagglutinin. These results provide the molecular basis for Vip3 activation and function, and serves as a strong foundation for the development of more efficient insecticidal proteins.


  • Organizational Affiliation

    Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040, Madrid, Spain. earias@cib.csic.es.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vegetative insecticidal protein
A, B, C, D
789Bacillus thuringiensisMutation(s): 0 
Gene Names: vip3LB
UniProt
Find proteins for Q58XI2 (Bacillus thuringiensis)
Explore Q58XI2 
Go to UniProtKB:  Q58XI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58XI2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2017-89143-P
Spanish Ministry of Economy and CompetitivenessSpainRYC-2015-19059
Spanish Ministry of Economy and CompetitivenessSpainBFU2016-78606-P
Spanish Ministry of Economy and CompetitivenessSpainRYC-2014-16490
Spanish Ministry of Science, Innovation, and UniversitiesSpainRTI2018-095204-B-C21

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-08-26
    Changes: Database references, Structure summary