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- EMDB-13946: Cryo-EM structure of Botulinum neurotoxin serotype E -

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Basic information

Entry
Database: EMDB / ID: EMD-13946
TitleCryo-EM structure of Botulinum neurotoxin serotype E
Map data
Sample
  • Complex: Botulinum neurotoxin serotype E
    • Protein or peptide: Botulinum neurotoxin
Function / homology
Function and homology information


negative regulation of neurotransmitter secretion / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / zinc ion binding / extracellular region
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Botulinum neurotoxin
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKosenina S / Martinez-Carranza M / Davies JR / Masuyer G / Stenmark P
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research Council2018-03406 Sweden
Cancerfonden20 1287 PjF Sweden
CitationJournal: Toxins (Basel) / Year: 2021
Title: Structural Analysis of Botulinum Neurotoxins Type B and E by Cryo-EM.
Authors: Sara Košenina / Markel Martínez-Carranza / Jonathan R Davies / Geoffrey Masuyer / Pål Stenmark /
Abstract: Botulinum neurotoxins (BoNTs) are the causative agents of a potentially lethal paralytic disease targeting cholinergic nerve terminals. Multiple BoNT serotypes exist, with types A, B and E being the ...Botulinum neurotoxins (BoNTs) are the causative agents of a potentially lethal paralytic disease targeting cholinergic nerve terminals. Multiple BoNT serotypes exist, with types A, B and E being the main cause of human botulism. Their extreme toxicity has been exploited for cosmetic and therapeutic uses to treat a wide range of neuromuscular disorders. Although naturally occurring BoNT types share a common end effect, their activity varies significantly based on the neuronal cell-surface receptors and intracellular SNARE substrates they target. These properties are the result of structural variations that have traditionally been studied using biophysical methods such as X-ray crystallography. Here, we determined the first structures of botulinum neurotoxins using single-particle cryogenic electron microscopy. The maps obtained at 3.6 and 3.7 Å for BoNT/B and /E, respectively, highlight the subtle structural dynamism between domains, and of the binding domain in particular. This study demonstrates how the recent advances made in the field of single-particle electron microscopy can be applied to bacterial toxins of clinical relevance and the botulinum neurotoxin family in particular.
History
DepositionDec 6, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateFeb 2, 2022-
Current statusFeb 2, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7qfp
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13946.png

Downloads & links

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Map

FileDownload / File: emd_13946.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 288 pix.
= 247.68 Å		0.86 Å/pix.
x 288 pix.
= 247.68 Å		0.86 Å/pix.
x 288 pix.
= 247.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.127 / Movie #1: 0.127
Minimum - Maximum-0.3967187 - 0.84011376
Average (Standard dev.)-0.0019283146 (±0.025618473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 247.68001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z247.680247.680247.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.3970.840-0.002

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Supplemental data

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Half map: #2

Fileemd_13946_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13946_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Botulinum neurotoxin serotype E

EntireName: Botulinum neurotoxin serotype E
Components
  • Complex: Botulinum neurotoxin serotype E
    • Protein or peptide: Botulinum neurotoxin

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Supramolecule #1: Botulinum neurotoxin serotype E

SupramoleculeName: Botulinum neurotoxin serotype E / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Botulinum neurotoxin

MacromoleculeName: Botulinum neurotoxin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 145.987438 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGHHHHHHHH HEDLYFQSPK INSFNYNDPV NDRTILYIKP GGCQEFYKSF NIMKNIWIIP ERNVIGTTPQ DFHPPTSLKN GDSSYYDPN YLQSDEEKDR FLKIVTKIFN RINNNLSGGI LLEELSKANP YLGNDNTPDN QFHIGDASAV EIKFSNGSQD I LLPNVIIM ...String:
MGHHHHHHHH HEDLYFQSPK INSFNYNDPV NDRTILYIKP GGCQEFYKSF NIMKNIWIIP ERNVIGTTPQ DFHPPTSLKN GDSSYYDPN YLQSDEEKDR FLKIVTKIFN RINNNLSGGI LLEELSKANP YLGNDNTPDN QFHIGDASAV EIKFSNGSQD I LLPNVIIM GAEPDLFETN SSNISLRNNY MPSNHGFGSI AIVTFSPEYS FRFNDNSMNE FIQDPALTLM HQLIYSLHGL YG AKGITTK YTITQKQNPL ITNIRGTNIE EFLTFGGTDL NIITSAQSND IYTNLLADYK KIASKLSKVQ VSNPLLNPYK DVF EAKYGL DKDASGIYSV NINKFNDIFK KLYSFTEFDL ATKFQVKCRQ TYIGQYKYFK LSNLLNDSIY NISEGYNINN LKVN FRGQN ANLNPRIITP ITGRGLVKKI IRFCKNIVSV KGIRKSICIE INNGELFFVA SENSYNDDNI NTPKEIDDTV TSNNN YEND LDQVILNFNS ESAPGLSDEK LNLTIQNDAY IPKYDSNGTS DIEQHDVNEL NVFFYLDAQK VPEGENNVNL TSSIDT ALL EQPKIYTFFS SEFINNVNKP VQAALFVSWI QQVLVDFTTE ANQKSTVDKI ADISIVVPYI GLALNIGNEA QKGNFKD AL ELLGAGILLE FEPELLIPTI LVFTIKSFLG SSDNKNKVIK AINNALKERD EKWKEVYSFI VSNWMTKINT QFNKRKEQ M YQALQNQVNA IKTIIESKYN SYTLEEKNEL TNKYDIKQIE NELNQKVSIA MNNIDRFLTE SSISYLMKLI NEVKINKLR EYDENVKTYL LNYIIQHGSI LGESQQELNS MVTDTLNNSI PFKLSSYTDD KILISYFNKF FKRIKSSSVL NMRYKNDKYV DTSGYDSNI NINGDVYKYP TNKNQFGIYN DKLSEVNISQ NDYIIYDNKY KNFSISFWVR IPNYDNKIVN VNNEYTIINC M RDNNSGWK VSLNHNEIIW TLQDNAGINQ KLAFNYGNAN GISDYINKWI FVTITNDRLG DSKLYINGNL IDQKSILNLG NI HVSDNIL FKIVNCSYTR YIGIRYFNIF DKELDETEIQ TLYSNEPNTN ILKDFWGNYL LYDKEYYLLN VLKPNNFIDR RKD STLSIN NIRSTILLAN RLYSGIKVKI QRVNNSSTND NLVRKNDQVY INFVASKTHL FPLYADTATT NKEKTIKISS SGNR FNQVV VMNSVGNNCT MNFKNNNGNN IGLLGFKADT VVASTWYYTH MRDHTNSNGC FWNFISEEHG WQEK

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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

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES pH 7.2, 200 mM NaCl, 1 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 200 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 18282 / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1096741
CTF correctionSoftware - Name: cryoSPARC (ver. 3.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final 3D classificationNumber classes: 15 / Software - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 284390
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7qfp:
Cryo-EM structure of Botulinum neurotoxin serotype E

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