[English] 日本語
Yorodumi
- EMDB-10492: Vip3Aa protoxin structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10492
TitleVip3Aa protoxin structure
Map dataHalf map 2
Sample
  • Complex: Vip3Aa protoxin
    • Protein or peptide: Vegetative insecticidal protein
KeywordsVip3Aa / toxin / protoxin / beta prism / insecticidal protein / Vip3
Function / homologyVegetative insecticide protein 3 / Vegetative insecticide protein 3A N terminal / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / hydrolase activity, acting on glycosyl bonds / Galactose-binding-like domain superfamily / Vegetative insecticidal protein
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsNunez-Ramirez R / Huesa J
Funding support Spain, 5 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2017-89143-P Spain
Spanish Ministry of Economy and CompetitivenessRYC-2015-19059 Spain
Spanish Ministry of Economy and CompetitivenessBFU2016-78606-P Spain
Spanish Ministry of Economy and CompetitivenessRYC-2014-16490 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-095204-B-C21 Spain
CitationJournal: 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.
History
DepositionNov 14, 2019-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6tfj
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10492.png

Downloads & links

-
Map

FileDownload / File: emd_10492.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHalf map 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 264 pix.
= 276.672 Å		1.05 Å/pix.
x 264 pix.
= 276.672 Å		1.05 Å/pix.
x 264 pix.
= 276.672 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.025
Minimum - Maximum-0.14471115 - 0.24508579
Average (Standard dev.)0.00032655618 (±0.005373959)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 276.672 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z276.672276.672276.672
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-0.1450.2450.000

-
Supplemental data

-
Mask #1

Fileemd_10492_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened EM map of the Vip3Aa protoxin

Fileemd_10492_additional_1.map
AnnotationUnsharpened EM map of the Vip3Aa protoxin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focused classification map of the C-terminal domains of the protoxin

Fileemd_10492_additional_2.map
AnnotationFocused classification map of the C-terminal domains of the protoxin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_10492_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Focused classification map of the C-terminal domains of the protoxin

Fileemd_10492_half_map_2.map
AnnotationFocused classification map of the C-terminal domains of the protoxin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Vip3Aa protoxin

EntireName: Vip3Aa protoxin
Components
  • Complex: Vip3Aa protoxin
    • Protein or peptide: Vegetative insecticidal protein

-
Supramolecule #1: Vip3Aa protoxin

SupramoleculeName: Vip3Aa protoxin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus thuringiensis (bacteria)
Molecular weightTheoretical: 350 KDa

-
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: 88.762805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKNNTKLST RALPSFIDYF NGIYGFATGI KDIMNMIFKT DTGGDLTLDE ILKNQQLLND ISGKLDGVNG SLNDLIAQGN LNTELSKEI LKIANEQNQV LNDVNNKLDA INTMLRVYLP KLTSMLSDVM KQNYALSLQI EYLSKQLQEI SDKLDIINVN V LINSTLTE ...String:
MNKNNTKLST RALPSFIDYF NGIYGFATGI KDIMNMIFKT DTGGDLTLDE ILKNQQLLND ISGKLDGVNG SLNDLIAQGN LNTELSKEI LKIANEQNQV LNDVNNKLDA INTMLRVYLP KLTSMLSDVM KQNYALSLQI EYLSKQLQEI SDKLDIINVN V LINSTLTE ITPAYQRIKY VNEKFEELTF ATETSSKVKK DGSPADILDE LTELTELAKS VTKNDVDGFE FYLNTFHDVM VG NNLFGRS ALKTASELIT KENVKTSGSE VGNVYNFLIV LTALQAKAFL TLTTCRKLLG LADIDYTSIM NEHLNKEKEE FRV NILPTL SNTFSNPNYA KVKGSDEDAK MIVEAKPGHA LIGFEISNDS ITVLKVYEAK LKQNYQVDKD SLSEVIYGDM DKLL CPDQS EQIYYTNNIV FPNEYVITKI DFTKKMKTLR YEVTANFYDS STGEIDLNKK KVESSEAEYR TLSANDDGVY MPLGV ISET FLTPINGFGL QADENSRLIT LTCKSYLREL LLATDLSNKE TKLIVPPSGF ISNIVENGSI EEDNLEPWKA NNKNAY VDH TGGVNGTKAL YVHKDGGISQ FIGDKLKPKT EYVIQYTVKG KPSIHLKDEN TGYIHYEDTN NNLEDYQTIN KRFTTGT DL KGVYLILKSQ NGDEAWGDNF IILEISPSEK LLSPELINTN NWTSTGSTNI SGNTLTLYQG GRGILKQNLQ LDSFSTYR V YFSVSGDANV RIRNSREVLF EKRYMSGAKD VSEMFTTKFE KDNFYIELSQ GNNLYGGPIV HFYDVSIK

UniProtKB: Vegetative insecticidal protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 56.6 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

+
Image processing

Startup modelType of model: OTHER
Details: Initial model was obtained using the SGD algorithm implemented in RELION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 478797
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsThe 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
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6tfj:
Vip3Aa protoxin structure

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more