[English] 日本語
Yorodumi
- EMDB-52734: HA70-HA17-HA33 complex from Botulinum neurotoxin serotype B1, foc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52734
TitleHA70-HA17-HA33 complex from Botulinum neurotoxin serotype B1, focused map of HA70 trimer
Map data
Sample
  • Complex: HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1
    • Complex: HA70 trimer
      • Protein or peptide: Hemagglutinin component HA70
      • Protein or peptide: Hemagglutinin component HA70
      • Protein or peptide: Hemagglutinin component HA70
    • Complex: HA17-HA33 subcomplex
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: 2.75 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_52734.png

Downloads & links

-
Map

FileDownload / File: emd_52734.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 320 pix.
= 416. Å		1.3 Å/pix.
x 320 pix.
= 416. Å		1.3 Å/pix.
x 320 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.161
Minimum - Maximum-0.47939345 - 1.1493038
Average (Standard dev.)-0.00023010233 (±0.016731048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_52734_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52734_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1

EntireName: HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1
Components
  • Complex: HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1
    • Complex: HA70 trimer
      • Protein or peptide: Hemagglutinin component HA70
      • Protein or peptide: Hemagglutinin component HA70
      • Protein or peptide: Hemagglutinin component HA70
    • Complex: HA17-HA33 subcomplex

-
Supramolecule #1: HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1

SupramoleculeName: HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 210 KDa

-
Supramolecule #2: HA70 trimer

SupramoleculeName: HA70 trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all

-
Supramolecule #3: HA17-HA33 subcomplex

SupramoleculeName: HA17-HA33 subcomplex / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Clostridium botulinum (bacteria)

-
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 EEYIKNNIQ TVFANFTEAN QIPIGFEFSK TAPSNKNLYM YLQYTYIRYE IIKVLQHEII ERAVLYVPSL GYVKSIEFNP G EKINKDFY ...String:
MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQ TVFANFTEAN QIPIGFEFSK TAPSNKNLYM YLQYTYIRYE IIKVLQHEII ERAVLYVPSL GYVKSIEFNP G EKINKDFY FLTNDKCILN EQFLYKKILE TTKNIPTNNI FNSKVSSTQR VLPYSNGLYV INKGDGYIRT NDKDLIGTLL IE AGSSGSI IQPRLRNTTR PLFTTSNDAK FSQQYTEERL KDAFNVQLFN TSTSLFKFVE EAPSNKNICI KAYNTYEKYE LID YQNGSI VNKAEYYLPS LGYCEVTNAP SPESEVVKTQ VAEDGFIQNG PEEEIVVGVI DPSENIQEIN TAISDNYTYN IPGI VNNNP FYILFTVNTT GIYKINAQNN LPSLKIYEAI GSGNRNFQSG NLCDDDIKAI NYITGFDSPN AKSYLVVLLN KDKNY YIRV PQTSSNIENQ IKFKREEGDL RNLMNSSVNI IDNLNSTGAH YYTRQSPDVH DYISYEFTIP GNFNNKDTSN IRLYTS YNQ GIGTLFRVTE TIDGYNLINI QQNLNLLNST KSIRLLNGAI YILKVEVTEL NNYNIKLHID ITN

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 EEYIKNNIQ TVFANFTEAN QIPIGFEFSK TAPSNKNLYM YLQYTYIRYE IIKVLQHEII ERAVLYVPSL GYVKSIEFNP G EKINKDFY ...String:
MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQ TVFANFTEAN QIPIGFEFSK TAPSNKNLYM YLQYTYIRYE IIKVLQHEII ERAVLYVPSL GYVKSIEFNP G EKINKDFY FLTNDKCILN EQFLYKKILE TTKNIPTNNI FNSKVSSTQR VLPYSNGLYV INKGDGYIRT NDKDLIGTLL IE AGSSGSI IQPRLRNTTR PLFTTSNDAK FSQQYTEERL KDAFNVQLFN TSTSLFKFVE EAPSNKNICI KAYNTYEKYE LID YQNGSI VNKAEYYLPS LGYCEVTNAP SPESEVVKTQ VAEDGFIQNG PEEEIVVGVI DPSENIQEIN TAISDNYTYN IPGI VNNNP FYILFTVNTT GIYKINAQNN LPSLKIYEAI GSGNRNFQSG NLCDDDIKAI NYITGFDSPN AKSYLVVLLN KDKNY YIRV PQTSSNIENQ IKFKREEGDL RNLMNSSVNI IDNLNSTGAH YYTRQSPDVH DYISYEFTIP GNFNNKDTSN IRLYTS YNQ GIGTLFRVTE TIDGYNLINI QQNLNLLNST KSIRLLNGAI YILKVEVTEL NNYNIKLHID ITN

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 EEYIKNNIQ TVFANFTEAN QIPIGFEFSK TAPSNKNLYM YLQYTYIRYE IIKVLQHEII ERAVLYVPSL GYVKSIEFNP G EKINKDFY ...String:
MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQ TVFANFTEAN QIPIGFEFSK TAPSNKNLYM YLQYTYIRYE IIKVLQHEII ERAVLYVPSL GYVKSIEFNP G EKINKDFY FLTNDKCILN EQFLYKKILE TTKNIPTNNI FNSKVSSTQR VLPYSNGLYV INKGDGYIRT NDKDLIGTLL IE AGSSGSI IQPRLRNTTR PLFTTSNDAK FSQQYTEERL KDAFNVQLFN TSTSLFKFVE EAPSNKNICI KAYNTYEKYE LID YQNGSI VNKAEYYLPS LGYCEVTNAP SPESEVVKTQ VAEDGFIQNG PEEEIVVGVI DPSENIQEIN TAISDNYTYN IPGI VNNNP FYILFTVNTT GIYKINAQNN LPSLKIYEAI GSGNRNFQSG NLCDDDIKAI NYITGFDSPN AKSYLVVLLN KDKNY YIRV PQTSSNIENQ IKFKREEGDL RNLMNSSVNI IDNLNSTGAH YYTRQSPDVH DYISYEFTIP GNFNNKDTSN IRLYTS YNQ GIGTLFRVTE TIDGYNLINI QQNLNLLNST KSIRLLNGAI YILKVEVTEL NNYNIKLHID ITN

UniProtKB: Hemagglutinin component HA70

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 130000
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: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 524091
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