[English] 日本語
Yorodumi
- EMDB-52742: L-PTC from Clostridium botulinum serotype B1, focused map of HA70... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52742
TitleL-PTC from Clostridium botulinum serotype B1, focused map of HA70 subcomplex
Map data
Sample
  • Complex: HA70 subcomplex from Clostridium botulinum serotype B1
    • Protein or peptide: Hemagglutinin component HA70
    • Protein or peptide: Hemagglutinin component HA70
    • Protein or peptide: Hemagglutinin component HA70
Keywordsprogenitor-toxin complex / botulinum neurotoxin / hemagglutinin / TOXIN
Function / homologyHemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium enterotoxin / Clostridium enterotoxin / extracellular region / Hemagglutinin component HA70
Function and homology information
Biological speciesClostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsKrc A / Persson Kosenina S / Masuyer G / Stenmark P
Funding support Sweden, Denmark, 2 items
OrganizationGrant numberCountry
Swedish Research Council2022-03681 Sweden
Novo Nordisk FoundationNNF20OC0064789 Denmark
CitationJournal: Sci Adv / Year: 2025
Title: Structure of the complete 14-subunit botulinum neurotoxin B complex reveals a unique anchoring through the narrow central pore of HA70.
Authors: Ajda Krč / Sara Persson Košenina / Maria B Nowakowska / Geoffrey Masuyer / Pål Stenmark /
Abstract: Botulinum neurotoxin serotype B1 (BoNT/B) is a highly potent neurotoxin and therapeutic agent. Here, we present the structure of the complete 14-subunit (780 kDa) progenitor toxin complex (L-PTC) and ...Botulinum neurotoxin serotype B1 (BoNT/B) is a highly potent neurotoxin and therapeutic agent. Here, we present the structure of the complete 14-subunit (780 kDa) progenitor toxin complex (L-PTC) and of five subcomplexes. The structures show how the toxin interacts with its associated components in their role to protect and deliver BoNT/B across epithelial barriers. Each subcomplex, including the M-PTC, M-PTC-HA70, NTNH-HA70, and HA70 trimer, provides detailed understanding of the assembly mechanism, in which the NTNH-nLoop adopts a unique fold that locks the M-PTC into a central pore formed by HA70. The HA subcomplex presents a tripod architecture with flexible legs that may adapt to the rugged cell surface. Mass photometry reveals the pH dependence of BoNT/B release from the complex which is unexpectedly influenced by the presence of HA70. This study provides the complete L-PTC structure, offering insights into its assemblage and supporting the development of countermeasures and therapeutic applications.
History
DepositionFeb 5, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52742.png

Downloads & links

-
Map

FileDownload / File: emd_52742.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 540 pix.
= 659.988 Å		1.22 Å/pix.
x 540 pix.
= 659.988 Å		1.22 Å/pix.
x 540 pix.
= 659.988 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2222 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.183
Minimum - Maximum-0.6769227 - 1.5270916
Average (Standard dev.)-0.00081835623 (±0.018771704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 659.98804 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_52742_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52742_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HA70 subcomplex from Clostridium botulinum serotype B1

EntireName: HA70 subcomplex from Clostridium botulinum serotype B1
Components
  • Complex: HA70 subcomplex from Clostridium botulinum serotype B1
    • Protein or peptide: Hemagglutinin component HA70
    • Protein or peptide: Hemagglutinin component HA70
    • Protein or peptide: Hemagglutinin component HA70

-
Supramolecule #1: HA70 subcomplex from Clostridium botulinum serotype B1

SupramoleculeName: HA70 subcomplex from Clostridium botulinum serotype B1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 210 KDa

-
Macromolecule #1: Hemagglutinin component HA70

MacromoleculeName: Hemagglutinin component HA70 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQT VFANFTEANQ IPIGFEFSKT APSNKNLYMY LQYTYIRYEI IKVLQHEIIE RAVLYVPSLG YVKSIEFNPG EKINKDFYFL ...String:
MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQT VFANFTEANQ IPIGFEFSKT APSNKNLYMY LQYTYIRYEI IKVLQHEIIE RAVLYVPSLG YVKSIEFNPG EKINKDFYFL TNDKCILNEQ FLYKKILETT KNIPTNNIFN SKVSSTQRVL PYSNGLYVIN KGDGYIRTND KDLIGTLLIE AGSSGSIIQP RLRNTTRPLF TTSNDAKFSQ QYTEERLKDA FNVQLFNTST SLFKFVEEAP SNKNICIKAY NTYEKYELID YQNGSIVNKA EYYLPSLGYC EVTNAPSPES EVVKTQVAED GFIQNGPEEE IVVGVIDPSE NIQEINTAIS DNYTYNIPGI VNNNPFYILF TVNTTGIYKI NAQNNLPSLK IYEAIGSGNR NFQSGNLCDD DIKAINYITG FDSPNAKSYL VVLLNKDKNY YIRVPQTSSN IENQIKFKRE EGDLRNLMNS SVNIIDNLNS TGAHYYTRQS PDVHDYISYE FTIPGNFNNK DTSNIRLYTS YNQGIGTLFR VTETIDGYNL INIQQNLNLL NSTKSIRLLN GAIYILKVEV TELNNYNIKL HIDITN

UniProtKB: Hemagglutinin component HA70

-
Macromolecule #2: Hemagglutinin component HA70

MacromoleculeName: Hemagglutinin component HA70 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQT VFANFTEANQ IPIGFEFSKT APSNKNLYMY LQYTYIRYEI IKVLQHEIIE RAVLYVPSLG YVKSIEFNPG EKINKDFYFL ...String:
MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQT VFANFTEANQ IPIGFEFSKT APSNKNLYMY LQYTYIRYEI IKVLQHEIIE RAVLYVPSLG YVKSIEFNPG EKINKDFYFL TNDKCILNEQ FLYKKILETT KNIPTNNIFN SKVSSTQRVL PYSNGLYVIN KGDGYIRTND KDLIGTLLIE AGSSGSIIQP RLRNTTRPLF TTSNDAKFSQ QYTEERLKDA FNVQLFNTST SLFKFVEEAP SNKNICIKAY NTYEKYELID YQNGSIVNKA EYYLPSLGYC EVTNAPSPES EVVKTQVAED GFIQNGPEEE IVVGVIDPSE NIQEINTAIS DNYTYNIPGI VNNNPFYILF TVNTTGIYKI NAQNNLPSLK IYEAIGSGNR NFQSGNLCDD DIKAINYITG FDSPNAKSYL VVLLNKDKNY YIRVPQTSSN IENQIKFKRE EGDLRNLMNS SVNIIDNLNS TGAHYYTRQS PDVHDYISYE FTIPGNFNNK DTSNIRLYTS YNQGIGTLFR VTETIDGYNL INIQQNLNLL NSTKSIRLLN GAIYILKVEV TELNNYNIKL HIDITN

UniProtKB: Hemagglutinin component HA70

-
Macromolecule #3: Hemagglutinin component HA70

MacromoleculeName: Hemagglutinin component HA70 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQT VFANFTEANQ IPIGFEFSKT APSNKNLYMY LQYTYIRYEI IKVLQHEIIE RAVLYVPSLG YVKSIEFNPG EKINKDFYFL ...String:
MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQT VFANFTEANQ IPIGFEFSKT APSNKNLYMY LQYTYIRYEI IKVLQHEIIE RAVLYVPSLG YVKSIEFNPG EKINKDFYFL TNDKCILNEQ FLYKKILETT KNIPTNNIFN SKVSSTQRVL PYSNGLYVIN KGDGYIRTND KDLIGTLLIE AGSSGSIIQP RLRNTTRPLF TTSNDAKFSQ QYTEERLKDA FNVQLFNTST SLFKFVEEAP SNKNICIKAY NTYEKYELID YQNGSIVNKA EYYLPSLGYC EVTNAPSPES EVVKTQVAED GFIQNGPEEE IVVGVIDPSE NIQEINTAIS DNYTYNIPGI VNNNPFYILF TVNTTGIYKI NAQNNLPSLK IYEAIGSGNR NFQSGNLCDD DIKAINYITG FDSPNAKSYL VVLLNKDKNY YIRVPQTSSN IENQIKFKRE EGDLRNLMNS SVNIIDNLNS TGAHYYTRQS PDVHDYISYE FTIPGNFNNK DTSNIRLYTS YNQGIGTLFR VTETIDGYNL INIQQNLNLL NSTKSIRLLN GAIYILKVEV TELNNYNIKL HIDITN

UniProtKB: Hemagglutinin component HA70

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Details: Graphene oxide coating
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139594
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more