+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10888 | |||||||||
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Title | Vip3Bc1 tetramer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Toxin / Vip3 / Bt toxin | |||||||||
Function / homology | Vegetative insecticide protein 3 / Vegetative insecticide protein 3A N terminal / Vegetative insecticidal protein Function and homology information | |||||||||
Biological species | Bacillus thuringiensis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Thompson RF / Byrne MJ | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10888.map.gz | 66 MB | EMDB map data format | |
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Header (meta data) | emd-10888-v30.xml emd-10888.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10888_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_10888.png | 121.2 KB | ||
Filedesc metadata | emd-10888.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10888 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10888 | HTTPS FTP |
-Validation report
Summary document | emd_10888_validation.pdf.gz | 264.6 KB | Display | EMDB validaton report |
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Full document | emd_10888_full_validation.pdf.gz | 263.7 KB | Display | |
Data in XML | emd_10888_validation.xml.gz | 11.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10888 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10888 | HTTPS FTP |
-Related structure data
Related structure data | 6yrfMC 6yrgC 7ntxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10888.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tetrameric assembly of Vip3Bc1
Entire | Name: Tetrameric assembly of Vip3Bc1 |
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Components |
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-Supramolecule #1: Tetrameric assembly of Vip3Bc1
Supramolecule | Name: Tetrameric assembly of Vip3Bc1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
-Macromolecule #1: Vegetative insecticidal protein
Macromolecule | Name: Vegetative insecticidal protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus thuringiensis (bacteria) |
Molecular weight | Theoretical: 91.287148 KDa |
Recombinant expression | Organism: Pseudomonas fluorescens (bacteria) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average exposure time: 1.5 sec. / Average electron dose: 76.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |