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- EMDB-16330: Botulinum neurotoxin serotype X in complex with NTNH/X -

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Basic information

Entry
Database: EMDB / ID: EMD-16330
TitleBotulinum neurotoxin serotype X in complex with NTNH/X
Map data
Sample
  • Complex: Botulinum neurotoxin serotype X in complex with NTNH/X
    • Protein or peptide: NTNH/X
    • Protein or peptide: Botulinum neurotoxin type X
KeywordsBotulinum neurotoxin / botulism / 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 / zinc ion binding ...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 / zinc ion binding / extracellular region / membrane
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 type X
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsMartinez-Carranza M / Skerlova J / Stenmark P
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.2.69/0.0/0.0/16_027/0008477European Union
CitationJournal: bioRxiv / Year: 2023
Title: Structure and activity of botulinum neurotoxin X.
Authors: Markel Martínez-Carranza / Jana Škerlová / Pyung-Gang Lee / Jie Zhang / Dave Burgin / Mark Elliott / Jules Philippe / Sarah Donald / Fraser Hornby / Linda Henriksson / Geoffrey Masuyer / ...Authors: Markel Martínez-Carranza / Jana Škerlová / Pyung-Gang Lee / Jie Zhang / Dave Burgin / Mark Elliott / Jules Philippe / Sarah Donald / Fraser Hornby / Linda Henriksson / Geoffrey Masuyer / Matthew Beard / Min Dong / Pål Stenmark
Abstract: Botulinum neurotoxins (BoNTs) are the most potent toxins known and are used to treat an increasing number of medical disorders. All BoNTs are naturally co-expressed with a protective partner protein ...Botulinum neurotoxins (BoNTs) are the most potent toxins known and are used to treat an increasing number of medical disorders. All BoNTs are naturally co-expressed with a protective partner protein (NTNH) with which they form a 300 kDa complex, to resist acidic and proteolytic attack from the digestive tract. We have previously identified a new botulinum neurotoxin serotype, BoNT/X, that has unique and therapeutically attractive properties. We present the cryo-EM structure of the BoNT/X-NTNH/X complex at 3.1 Å resolution. Unexpectedly, the BoNT/X complex is stable and protease resistant at both neutral and acidic pH and disassembles only in alkaline conditions. Using the stabilizing effect of NTNH, we isolated BoNT/X and showed that it has very low potency both and . Given the high catalytic activity and translocation efficacy of BoNT/X, low activity of the full toxin is likely due to the receptor-binding domain, which presents weak ganglioside binding and exposed hydrophobic surfaces.
History
DepositionDec 15, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16330.png

Downloads & links

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Map

FileDownload / File: emd_16330.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.26634 - 3.8607788
Average (Standard dev.)0.0015429693 (±0.15424018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16330_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16330_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16330_half_map_2.map
Projections & Slices
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Sample components

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Entire : Botulinum neurotoxin serotype X in complex with NTNH/X

EntireName: Botulinum neurotoxin serotype X in complex with NTNH/X
Components
  • Complex: Botulinum neurotoxin serotype X in complex with NTNH/X
    • Protein or peptide: NTNH/X
    • Protein or peptide: Botulinum neurotoxin type X

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Supramolecule #1: Botulinum neurotoxin serotype X in complex with NTNH/X

SupramoleculeName: Botulinum neurotoxin serotype X in complex with NTNH/X
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: NTNH/X

MacromoleculeName: NTNH/X / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 137.394984 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDINDKLSID SPIDNKNIIE FITFRTDTSG IQKKIKAYQI AKHIWVVPER YYAEPLNISD EYKIDGGIYN ENYLTTDKER QEYLDAICI LFKRINNVIE GKKLLSLLSS ASPFPFKDDT NKYLLKEALL YVNEENFEFK FFTSNIILFG PGTNISKNQV L PLNGDDAT ...String:
MDINDKLSID SPIDNKNIIE FITFRTDTSG IQKKIKAYQI AKHIWVVPER YYAEPLNISD EYKIDGGIYN ENYLTTDKER QEYLDAICI LFKRINNVIE GKKLLSLLSS ASPFPFKDDT NKYLLKEALL YVNEENFEFK FFTSNIILFG PGTNISKNQV L PLNGDDAT SGVGSVSEIC YNPFFTKKFG EYSLDPVIGL IECLLKSLYN LYGIKVSDDI KIPYKLQRAL NTDKYSYINL EE ALIFGGN DYKIFTEKPY WLSNDYFLKS LNTFEENKAK YEKDLKNDPN LNNELNQYLQ QKYSFSISKI WSLNLTAFAD IFN INIPTS FLASITFWDR SQYYKINYPN DYNIDGFVNG QWNTNLKNIE KDNNFIIFDK PKQIITYIND IFNLRYTSNL YEDN LDIES NNYYLNFMFE YDKGNNFTIN QYKALLDTLD NDFIDSLPPI QGMNAQNKLT SLPIISKGTD TENINSELLL PIHYL KSQT YNLDMYSSIK FTTNIYEVVS EKNSELVYTF LPHINEIMEN YSINNTIKTE EEFYNWMENL FINYSIDILE KRNSII PGI TAVLPWIGKA LNILNTNNDF EEELQLSGIK GLIKEYENFI IPDMIVPDIP LDNMPRTYDD IDKKLSEIYT KNKFLFL KG YYFIVQEWWT TYYIQFIELK YLCSGAINKQ QQLLITVLEK QLFYFTNNGL FPFDAMERMI NEFNRSIDIF SRISQQAL N NVDIFINECA LFIFNNEVYP LFLNNVENNI NKANDNVLNY INKATSLTEE QIKELTVKYT FSSIAEVEFF NESYFKKIT NMDIKNILTN IKNINNLILS GSQINDDITI FDESGNNLNI KFDPSIRIVD GHTNVAFKLD KSSQYINIPT ENINFSFMES FSIDFWLKI LDSTESTTLL NCIEDDIGWK LSIQNNNLLW EMKDNLGNNF TSLFTFNINN IWHNITLSID RLTNTFNCFL D GKLINTDN ISNIFSLETN TPIEIQSDNG AILLEAFSIL NYPLQQQEVL NRYREAFSNN YTRNYYGDIL KYNENYQLYN KT SPDKEVK KVFTNDKDYI AIEYNQNTNN PTFFSLIQKE QSKIYVEEND EVYICVQGDP LNYITIDNNQ AVLTKDINLA TSF KLKTNL NKPNSLIFSE NSQALRLSNR LNDENYILLD LVSKLDDEPL NIFYWEFI

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Macromolecule #2: Botulinum neurotoxin type X

MacromoleculeName: Botulinum neurotoxin type X / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 150.348891 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKLEINKFNY NDPIDGINVI TMRPPRHSDK INKGKGPFKA FQVIKNIWIV PERYNFTNNT NDLNIPSEPI MEADAIYNPN YLNTPSEKD EFLQGVIKVL ERIKSKPEGE KLLELISSSI PLPLVSNGAL TLSDNETIAY QENNNIVSNL QANLVIYGPG P DIANNATY ...String:
MKLEINKFNY NDPIDGINVI TMRPPRHSDK INKGKGPFKA FQVIKNIWIV PERYNFTNNT NDLNIPSEPI MEADAIYNPN YLNTPSEKD EFLQGVIKVL ERIKSKPEGE KLLELISSSI PLPLVSNGAL TLSDNETIAY QENNNIVSNL QANLVIYGPG P DIANNATY GLYSTPISNG EGTLSEVSFS PFYLKPFDES YGNYRSLVNI VNKFVKREFA PDPASTLMHE LVHVTHNLYG IS NRNFYYN FDTGKIETSR QQNSLIFEEL LTFGGIDSKA ISSLIIKKII ETAKNNYTTL ISERLNTVTV ENDLLKYIKN KIP VQGRLG NFKLDTAEFE KKLNTILFVL NESNLAQRFS ILVAKHFLKE RPIDPIYVNI LDDNSYSTLE GFNISSQGSN DFQG QLLES SYFEKIESNA LRAFIKICPR NGLLYNAIYR NSKNYLNNID LEDKKTTSKT NVSYPCSLLN GCIEVENKDL FLISN KDSL NDINLSEEKI KPETTVFFKD KLPPQDITLS NYDFTEANSI PSISQQNILE RNEELYEPIR NSLFEIKTIY VDKLTT FHF LEAQNIDESI DSSKIRVELT DSVDEALSNP NKVYSPFKNM SNTINSIETG ITSTYIFYQW LRSIVKDFSD ETGKIDV ID KSSDTLAIVP YIGPLLNIGN DIRHGDFVGA IELAGITALL EYVPEFTIPI LVGLEVIGGE LAREQVEAIV NNALDKRD Q KWAEVYNITK AQWWGTIHLQ INTRLAHTYK ALSRQANAIK MNMEFQLANY KGNIDDKAKI KNAISETEIL LNKSVEQAM KNTEKFMIKL SNSYLTKEMI PKVQDNLKNF DLETKKTLDK FIKEKEDILG TNLSSSLRRK VSIRLNKNIA FDINDIPFSE FDDLINQYK NEIEDYEVLN LGAEDGKIKD LSGTTSDINI GSDIELADGR ENKAIKIKGS ENSTIKIAMN KYLRFSATDN F SISFWIKH PKPTNLLNNG IEYTLVENFN QRGWKISIQD SKLIWYLRDH NNSIKIVTPD YIAFNGWNLI TITNNRSKGS IV YVNGSKI EEKDISSIWN TEVDDPIIFR LKNNRDTQAF TLLDQFSIYR KELNQNEVVK LYNYYFNSNY IRDIWGNPLQ YNK KYYLQT QDKPGKGLIR EYWSSFGYDY VILSDSKTIT FPNNIRYGAL YNGSKVLIKN SKKLDGLVRN KDFIQLEIDG YNMG ISADR FNEDTNYIGT TYGTTHDLTT DFEIIQRQEK YRNYCQLKTP YNIFHKSGLM STETSKPTFH DYRDWVYSSA WYFQN YENL NLRKHTKTNW YFIPKDEGWD ED

UniProtKB: Botulinum neurotoxin type X

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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: 5.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3v0a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 432063
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8byp:
Botulinum neurotoxin serotype X in complex with NTNH/X

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