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- EMDB-51433: Cryo-EM structure of Botulinum neurotoxin serotype A -

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Basic information

Entry
Database: EMDB / ID: EMD-51433
TitleCryo-EM structure of Botulinum neurotoxin serotype A
Map data
Sample
  • Complex: Botulinum neurotoxin serotype A
    • Protein or peptide: Botulinum neurotoxin type A
KeywordsBotulinum neurotoxin serotype A / Cryo-EM / TOXIN
Function / homology
Function and homology information


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsZerang Z / Liu Z / He J / Wang X / Qi F / Lei D / Zhi D / Wang D
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073825 China
National Natural Science Foundation of China (NSFC)32171300 China
Other government22ZD6FA053
Other government20JR10RA619
Other governmentlzuyxcx-2022-197
CitationJournal: To Be Published
Title: Cryo-EM Structure guided engineering of botulinum neurotoxin A with advanced receptor binding affinity and therapeutical benefits
Authors: You L / Wang W / Zerang Z / Liu Z / Nie R / Zhao C / He J / Wang X / Qi F / Liu F / Wu S / Liu B / Lei D / Zhi D / Wang D
History
DepositionAug 26, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51433.png

Downloads & links

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Map

FileDownload / File: emd_51433.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.104 Å		0.83 Å/pix.
x 384 pix.
= 319.104 Å		0.83 Å/pix.
x 384 pix.
= 319.104 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.24
Minimum - Maximum-0.12368269 - 19.834776000000002
Average (Standard dev.)-0.029371629 (±0.34805742)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51433_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51433_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51433_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Botulinum neurotoxin serotype A

EntireName: Botulinum neurotoxin serotype A
Components
  • Complex: Botulinum neurotoxin serotype A
    • Protein or peptide: Botulinum neurotoxin type A

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Supramolecule #1: Botulinum neurotoxin serotype A

SupramoleculeName: Botulinum neurotoxin serotype A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium botulinum (bacteria)

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Macromolecule #1: Botulinum neurotoxin type A

MacromoleculeName: Botulinum neurotoxin type A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 151.022516 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPFVNKQFNY KDPVNGVDIA YIKIPNAGQM QPVKAFKIHN KIWVIPERDT FTNPEEGDLN PPPEAKQVPV SYYDSTYLST DNEKDNYLK GVTKLFERIY STDLGRMLLT SIVRGIPFWG GSTIDTELKV IDTNCINVIQ PDGSYRSEEL NLVIIGPSAD I IQFECKSF ...String:
MPFVNKQFNY KDPVNGVDIA YIKIPNAGQM QPVKAFKIHN KIWVIPERDT FTNPEEGDLN PPPEAKQVPV SYYDSTYLST DNEKDNYLK GVTKLFERIY STDLGRMLLT SIVRGIPFWG GSTIDTELKV IDTNCINVIQ PDGSYRSEEL NLVIIGPSAD I IQFECKSF GHEVLNLTRN GYGSTQYIRF SPDFTFGFEE SLEVDTNPLL GAGKFATDPA VTLAHELIHA GHRLYGIAIN PN RVFKVNT NAYYEMSGLE VSFEELRTFG GHDAKFIDSL QENEFRLYYY NKFKDIASTL NKAKSIVGTT ASLQYMKNVF KEK YLLSED TSGKFSVDKL KFDKLYKMLT EIYTEDNFVK FFKVLNRKTY LNFDKAVFKI NIVPKVNYTI YDGFNLRNTN LAAN FNGQN TEINNMNFTK LKNFTGLFEF YKLLCVRGII TSKTKSLDKG YNKALNDLCI KVNNWDLFFS PSEDNFTNDL NKGEE ITSD TNIEAAEENI SLDLIQQYYL TFNFDNEPEN ISIENLSSDI IGQLELMPNI ERFPNGKKYE LDKYTMFHYL RAQEFE HGK SRIALTNSVN EALLNPSRVY TFFSSDYVKK VNKATEAAMF LGWVEQLVYD FTDETSEVST TDKIADITII IPYIGPA LN IGNMLYKDDF VGALIFSGAV ILLEFIPEIA IPVLGTFALV SYIANKVLTV QTIDNALSKR NEKWDEVYKY IVTNWLAK V NTQIDLIRKK MKEALENQAE ATKAIINYQY NQYTEEEKNN INFNIDDLSS KLNESINKAM ININKFLNQC SVSYLMNSM IPYGVKRLED FDASLKDALL KYIYDNRGTL IGQVDRLKDK VNNTLSTDIP FQLSKYVDNQ RLLSTFTEYI KNIINTSILN LRYESNHLI DLSRYASKIN IGSKVNFDPI DKNQIQLFNL ESSKIEVILK NAIVYNSMYE NFSTSFWIRI PKYFNSISLN N EYTIINCM ENNSGWKVSL NYGEIIWTLQ DTQEIKQRVV FKYSQMINIS DYINRWIFVT ITNNRLNNSK IYINGRLIDQ KP ISNLGNI HASNNIMFKL DGCRDTHRYI WIKYFNLFDK ELNEKEIKDL YDNQSNSGIL KDFWGDYLQY DKPYYMLNLY DPN KYVDVN NVGIRGYMYL KGPRGSVMTT NIYLNSSLYR GTKFIIKKYA SGNKDNIVRN NDRVYINVVV KNKEYRLATN ASQA GVEKI LSALEIPDVG NLSQVVVMKS KNDQGITNKC KMNLQDNNGN DIGFIGFHQF NNIAKLVASN WYNRQIERSS RTLGC SWEF IPVDDGWGER PLLVPRGSHH HHHH

UniProtKB: Botulinum neurotoxin type A

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 336881
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-9gkq:
Cryo-EM structure of Botulinum neurotoxin serotype A

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