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- EMDB-13643: Delta-latroinsectotoxin dimer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-13643
TitleDelta-latroinsectotoxin dimer
Map data
Sample
  • Complex: Delta-latroinsectotoxin-Lt1a in soluble dimeric state
    • Protein or peptide: Delta-latroinsectotoxin-Lt1a
Function / homology
Function and homology information


exocytosis / toxin activity / membrane => GO:0016020 / extracellular region
Similarity search - Function
Domain of unknown function DUF3447 / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Delta-latroinsectotoxin-Lt1a
Similarity search - Component
Biological speciesLatrodectus tredecimguttatus (black widow)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.63 Å
AuthorsChen M / Gatsogiannis C
Funding support Japan, 3 items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Japan
Max Planck Society Japan
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2021
Title: Molecular architecture of black widow spider neurotoxins.
Authors: Minghao Chen / Daniel Blum / Lena Engelhard / Stefan Raunser / Richard Wagner / Christos Gatsogiannis /
Abstract: Latrotoxins (LaTXs) are presynaptic pore-forming neurotoxins found in the venom of Latrodectus spiders. The venom contains a toxic cocktail of seven LaTXs, with one of them targeting vertebrates (α- ...Latrotoxins (LaTXs) are presynaptic pore-forming neurotoxins found in the venom of Latrodectus spiders. The venom contains a toxic cocktail of seven LaTXs, with one of them targeting vertebrates (α-latrotoxin (α-LTX)), five specialized on insects (α, β, γ, δ, ε- latroinsectotoxins (LITs), and one on crustaceans (α-latrocrustatoxin (α-LCT)). LaTXs bind to specific receptors on the surface of neuronal cells, inducing the release of neurotransmitters either by directly stimulating exocytosis or by forming Ca-conductive tetrameric pores in the membrane. Despite extensive studies in the past decades, a high-resolution structure of a LaTX is not yet available and the precise mechanism of LaTX action remains unclear. Here, we report cryoEM structures of the α-LCT monomer and the δ-LIT dimer. The structures reveal that LaTXs are organized in four domains. A C-terminal domain of ankyrin-like repeats shields a central membrane insertion domain of six parallel α-helices. Both domains are flexibly linked via an N-terminal α-helical domain and a small β-sheet domain. A comparison between the structures suggests that oligomerization involves major conformational changes in LaTXs with longer C-terminal domains. Based on our data we propose a cyclic mechanism of oligomerization, taking place prior membrane insertion. Both recombinant α-LCT and δ-LIT form channels in artificial membrane bilayers, that are stabilized by Ca ions and allow calcium flux at negative membrane potentials. Our comparative analysis between α-LCT and δ-LIT provides first crucial insights towards understanding the molecular mechanism of the LaTX family.
History
DepositionSep 27, 2021-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateDec 8, 2021-
Current statusDec 8, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pty
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13643.png

Downloads & links

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Map

FileDownload / File: emd_13643.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 360 pix.
= 324. Å		0.9 Å/pix.
x 360 pix.
= 324. Å		0.9 Å/pix.
x 360 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003 / Movie #1: 0.0025
Minimum - Maximum-0.0027791257 - 0.009666656
Average (Standard dev.)2.7221877e-05 (±0.00028467513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.90.90.9
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.0030.0100.000

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Supplemental data

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Sample components

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Entire : Delta-latroinsectotoxin-Lt1a in soluble dimeric state

EntireName: Delta-latroinsectotoxin-Lt1a in soluble dimeric state
Components
  • Complex: Delta-latroinsectotoxin-Lt1a in soluble dimeric state
    • Protein or peptide: Delta-latroinsectotoxin-Lt1a

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Supramolecule #1: Delta-latroinsectotoxin-Lt1a in soluble dimeric state

SupramoleculeName: Delta-latroinsectotoxin-Lt1a in soluble dimeric state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Latrodectus tredecimguttatus (black widow)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 139.8 KDa

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Macromolecule #1: Delta-latroinsectotoxin-Lt1a

MacromoleculeName: Delta-latroinsectotoxin-Lt1a / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Latrodectus tredecimguttatus (black widow)
Molecular weightTheoretical: 145.047547 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKFLVNVALV FMVVYISYIY AMWSHPQFEK GSAGSAAGSG AGWSHPQFEK GAGLEVLFQG PPWMHSKELQ TISAAVARKA VPNTMVIRL KRDEEDGEMT LEERQAQCKA IEYSNSVFGM IADVANDIGS IPVIGEVVGI VTAPIAIVSH ITSAGLDIAS T ALDCDDIP ...String:
MKFLVNVALV FMVVYISYIY AMWSHPQFEK GSAGSAAGSG AGWSHPQFEK GAGLEVLFQG PPWMHSKELQ TISAAVARKA VPNTMVIRL KRDEEDGEMT LEERQAQCKA IEYSNSVFGM IADVANDIGS IPVIGEVVGI VTAPIAIVSH ITSAGLDIAS T ALDCDDIP FDEIKEILEE RFNEIDRKLD KNTAALEEVS KLVSKTFVTV EKTRNEMNEN FKLVLETIES KEIKSIVFKI ND FKKFFEK ERQRIKGLPK DRYVAKLLEQ KGILGSLKEV REPSGNSLSS ALNELLDKNN NYAIPKVVDD NKAFQALYAL FYG TQTYAA VMFFLLEQHS YLADYYYQKG DDVNFNAEFN NVAIIFDDFK SSLTGGDDGL IDNVIEVLNT VKALPFIKNA DSKL YRELV TRTKALETLK NQIKTTDLPL IDDIPETLSQ VNFPNDENQL PTPIGNWVDG VEVRYAVQYE SKGMYSKFSE WSEPF TVQG NACPTIKVRV DPKKRNRLIF RKFNSGKPQF AGTMTHSQTN FKDIHRDLYD AALNINKLKA VDEATTLIEK GADIEA KFD NDRSAMHAVA YRGNNKIALR FLLKNQSIDI ELKDKNGFTP LHIAAEAGQA GFVKLLINHG ADVNAKTSKT NLTPLHL AT RSGFSKTVRN LLESPNIKVN EKEDDGFTPL HTAVMSTYMV VDALLNHPDI DKNAQSTSGL TPFHLAIINE SQEVAESL V ESNADLNIQD VNHMAPIHFA ASMGSIKMLR YLISIKDKVS INSVTENNNW TPLHFAIYFK KEDAAKELLK QDDINLTIV ADGNLTVLHL AVSTGQINII KELLKRGSNI EEKTGEGYTS LHIAAMRKEP EIAVVLIENG ADIEARSADN LTPLHSAAKI GRKSTVLYL LEKGADIGAK TADGSTALHL AVSGRKMKTV ETLLNKGANL KEYDNNKYLP IHKAIINDDL DMVRLFLEKD P SLKDDETE EGRTSIMLIV QKLLLELYNY FINNYAETLD EEALFNRLDE QGKLELAYIF HNKEGDAKEA VKPTILVTIK LM EYCLKKL REESGAPEGS FDSPSSKQCI STFSEDEMFR RTLPEIVKET NSRYLPLKGF SRSLNKFLPS LKFAESKNSY RSE NFVSNI DSNGALLLLD VFIRKFTNEK YNLTGKEAVP YLEAKASSLR IASKFEELLT EVKGIPAGEL INMAEVSSNI HKAI ASGKP VSKVLCSYLD TFSELNSQQM EELVNTYLST KPSVITSASA DYQKLPNLLT ATCLEPERMA QLIDVHQKMF LRLES SGLV PRGSHHHHHH HH

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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

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMTris-HClTristrisaminomethane hydrochloride
150.0 mMNaClSodium chloridesodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acidEthylenediaminetetraacetic acid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 78.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE (ver. 1.3) / Number images used: 81192

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7pty:
Delta-latroinsectotoxin dimer

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