+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16330 | |||||||||
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Title | Botulinum neurotoxin serotype X in complex with NTNH/X | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Botulinum 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 | |||||||||
Biological species | Clostridium botulinum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||
Authors | Martinez-Carranza M / Skerlova J / Stenmark P | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16330.map.gz | 95.7 MB | EMDB map data format | |
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Header (meta data) | emd-16330-v30.xml emd-16330.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16330_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_16330.png | 99.5 KB | ||
Masks | emd_16330_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-16330.cif.gz | 6.9 KB | ||
Others | emd_16330_half_map_1.map.gz emd_16330_half_map_2.map.gz | 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16330 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16330 | HTTPS FTP |
-Validation report
Summary document | emd_16330_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_16330_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_16330_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | emd_16330_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16330 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16330 | HTTPS FTP |
-Related structure data
Related structure data | 8bypMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16330.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16330_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16330_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16330_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Botulinum neurotoxin serotype X in complex with NTNH/X
Entire | Name: Botulinum neurotoxin serotype X in complex with NTNH/X |
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Components |
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-Supramolecule #1: Botulinum neurotoxin serotype X in complex with NTNH/X
Supramolecule | Name: Botulinum neurotoxin serotype X in complex with NTNH/X type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Clostridium botulinum (bacteria) |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: NTNH/X
Macromolecule | Name: NTNH/X / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridium botulinum (bacteria) |
Molecular weight | Theoretical: 137.394984 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: Botulinum neurotoxin type X
Macromolecule | Name: Botulinum neurotoxin type X / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridium botulinum (bacteria) |
Molecular weight | Theoretical: 150.348891 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-8byp: |