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- EMDB-10889: Vip3Bc1 tetramer in processed, activated state -

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Basic information

Entry
Database: EMDB / ID: EMD-10889
TitleVip3Bc1 tetramer in processed, activated state
Map data
Sample
  • Complex: Tetrameric assembly of activated, processed Vip3Bc1
    • Protein or peptide: Vegetative insecticidal protein
KeywordsToxin / Vip3 / Bt toxin
Function / homologyVegetative insecticide protein 3 / Vegetative insecticide protein 3A N terminal / Vegetative insecticidal protein
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsThompson RF / Byrne MJ
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structures of an insecticidal Bt toxin reveal its mechanism of action on the membrane.
Authors: Matthew J Byrne / Matthew G Iadanza / Marcos Arribas Perez / Daniel P Maskell / Rachel M George / Emma L Hesketh / Paul A Beales / Marc D Zack / Colin Berry / Rebecca F Thompson /
Abstract: Insect pests are a major cause of crop losses worldwide, with an estimated economic cost of $470 billion annually. Biotechnological tools have been introduced to control such insects without the need ...Insect pests are a major cause of crop losses worldwide, with an estimated economic cost of $470 billion annually. Biotechnological tools have been introduced to control such insects without the need for chemical pesticides; for instance, the development of transgenic plants harbouring genes encoding insecticidal proteins. The Vip3 (vegetative insecticidal protein 3) family proteins from Bacillus thuringiensis convey toxicity to species within the Lepidoptera, and have wide potential applications in commercial agriculture. Vip3 proteins are proposed to exert their insecticidal activity through pore formation, though to date there is no mechanistic description of how this occurs on the membrane. Here we present cryo-EM structures of a Vip3 family toxin in both inactive and activated forms in conjunction with structural and functional data on toxin-membrane interactions. Together these data demonstrate that activated Vip3Bc1 complex is able to insert into membranes in a highly efficient manner, indicating that receptor binding is the likely driver of Vip3 specificity.
History
DepositionApr 20, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yrg
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ntx
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10889.png

Downloads & links

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Map

FileDownload / File: emd_10889.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.55 / Movie #1: 0.55
Minimum - Maximum-0.7874999 - 2.7787771
Average (Standard dev.)0.0052389805 (±0.0996259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 319.50003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z319.500319.500319.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.7872.7790.005

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Supplemental data

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Sample components

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Entire : Tetrameric assembly of activated, processed Vip3Bc1

EntireName: Tetrameric assembly of activated, processed Vip3Bc1
Components
  • Complex: Tetrameric assembly of activated, processed Vip3Bc1
    • Protein or peptide: Vegetative insecticidal protein

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Supramolecule #1: Tetrameric assembly of activated, processed Vip3Bc1

SupramoleculeName: Tetrameric assembly of activated, processed Vip3Bc1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus thuringiensis (bacteria)

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Macromolecule #1: Vegetative insecticidal protein

MacromoleculeName: Vegetative insecticidal protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus thuringiensis (bacteria)
Molecular weightTheoretical: 91.287148 KDa
Recombinant expressionOrganism: Pseudomonas fluorescens (bacteria)
SequenceString: MVQKWMQRMI IVDNNKLNVR ALPSFIDYFN GIYGFATGIK DIMGMIFKTD TGGSNLTLDE ILKNQNLLND ISGKLDGING DLGDLIAQG NLNSELAKEL LKISNEQNQM LNHVNAQLNA INSTLNIYLP KITSMLNEVM KQNHVLSLQI EFLSKQLQEI S DKLDIINL ...String:
MVQKWMQRMI IVDNNKLNVR ALPSFIDYFN GIYGFATGIK DIMGMIFKTD TGGSNLTLDE ILKNQNLLND ISGKLDGING DLGDLIAQG NLNSELAKEL LKISNEQNQM LNHVNAQLNA INSTLNIYLP KITSMLNEVM KQNHVLSLQI EFLSKQLQEI S DKLDIINL NVLINSTLTE ITPAYQRIKY VNEKFDELTS TVEKNPKSYQ DNVTKEVIEN LNELTELAKS VTKNDMDSFE FY LQTFHDV MTGNNLFGRS ALKTASELIT KENVTTRGSE IGKVYNFLIV LTSLQAKAFL TLTACRKLLG LTDIDYTQIM NHH IDGQKR EFRINILPTL SNNFSNPSYS KNRGSDIDDP IVVLEAAPGY ALIGFEILND PLPILKGYQA RLKPNYQVDR ESMS ETIYG DIHKLFCPKQ LEQKYYIKDI EFPEGYVITK IVFEKRLNQL GYEVTANFYD PSTGSIDLNK VKVESWKEKS CEEDS CEDE YSIIKAETDG IYMPLGVVSE TFLTPIYGFG LTVDEKNQKI TLTGKSYLRE SLLETDLLNN ETYLIASPDG YISSIV ENW NITSDNTGSW RANNNNAFVD KADTIKGSSS LYTHKDGEFS QFIGNKLKPK TNYVIQYVIK GRPAIYLKNN KDTLFED TK NNFSDFQTVT KKFNSGVNPS EIYFLFKNQS EYEAWGNNFI ILEIKSLEFL PQMLKPEDWI PSGNVQMKDG GRLEILGD G YFKQFIKLEN DSTYHLRLSV KGTGRVSIID ESKYLLFVNV KDEDLTRVIK NTSSKGECFI ALEGTYVENS STIFSNVSI VKE

UniProtKB: Vegetative insecticidal protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Detector mode: INTEGRATING / #0 - Number grids imaged: 1 / #0 - Average exposure time: 1.5 sec. / #0 - Average electron dose: 70.8 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON III (4k x 4k) / #1 - Detector mode: INTEGRATING / #1 - Average electron dose: 42.51 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 191975
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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