Spanish Ministry of Science, Innovation, and Universities
RTI2018-095204-B-C21
Spain
Citation
Journal: Nat Commun / Year: 2020 Title: Molecular architecture and activation of the insecticidal protein Vip3Aa from Bacillus thuringiensis. Authors: Rafael Núñez-Ramírez / Juanjo Huesa / Yolanda Bel / Juan Ferré / Patricia Casino / Ernesto Arias-Palomo / 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 ...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.
A: Vegetative insecticidal protein B: Vegetative insecticidal protein C: Vegetative insecticidal protein D: Vegetative insecticidal protein hetero molecules
Mass: 88762.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The sample was activated by trypsin digestion / Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: vip3LB / Production host: Escherichia coli (E. coli) / References: UniProt: Q58XI2
Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
-
Electron microscopy imaging
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
Microscopy
Model: FEI TITAN KRIOS
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens
Mode: BRIGHT FIELD
Image recording
Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
-
Processing
Software
Name
Version
Classification
phenix.real_space_refine
1.18rc6_3830
refinement
PHENIX
1.18rc6_3830
refinement
EM software
ID
Name
Version
Category
2
EPU
imageacquisition
4
Gctf
CTFcorrection
5
RELION
3
CTFcorrection
10
PHENIX
1.17
modelrefinement
11
RELION
3
initialEulerassignment
12
RELION
3
finalEulerassignment
14
RELION
3
3Dreconstruction
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
Point symmetry: C4 (4 fold cyclic)
3D reconstruction
Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92303 / Symmetry type: POINT
Atomic model building
Protocol: OTHER / Space: REAL Details: The atomic coordinates were manually modeled de novo in the cryo-EM map using Coot, and then subjected to iterative rounds of real space refinement using Phenix
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi