9QCE | pdb_00009qce

HA70-HA17-HA33 complex from Clostridium botulinum Serotype B1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Structure of the complete 14-subunit botulinum neurotoxin B complex reveals a unique anchoring through the narrow central pore of HA70.

Krc, A.Kosenina, S.P.Nowakowska, M.B.Masuyer, G.Stenmark, P.

(2025) Sci Adv 11: eadx5058-eadx5058

  • DOI: https://doi.org/10.1126/sciadv.adx5058
  • Primary Citation Related Structures: 
    9QC7, 9QC8, 9QCE, 9QCM, 9QCN, 9QCO

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 298.04 kDa 
  • Atom Count: 18,572 
  • Modeled Residue Count: 2,407 
  • Deposited Residue Count: 2,612 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin component HA70
A, B, C
626Clostridium botulinumMutation(s): 0 
Gene Names: ha70CLD_A0073
UniProt
Find proteins for B1INQ0 (Clostridium botulinum (strain Okra / Type B1))
Explore B1INQ0 
Go to UniProtKB:  B1INQ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1INQ0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin component HA17146Clostridium botulinumMutation(s): 0 
Gene Names: ha17CLD_A0072
UniProt
Find proteins for B1INP9 (Clostridium botulinum (strain Okra / Type B1))
Explore B1INP9 
Go to UniProtKB:  B1INP9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1INP9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin component HA33
E, F
294Clostridium botulinumMutation(s): 0 
Gene Names: ha33CLD_A0071
UniProt
Find proteins for B1INP8 (Clostridium botulinum (strain Okra / Type B1))
Explore B1INP8 
Go to UniProtKB:  B1INP8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1INP8
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2022-03681
Novo Nordisk FoundationDenmarkNNF20OC0064789

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release