1YBI | pdb_00001ybi

Crystal structure of HA33A, a neurotoxin-associated protein from Clostridium botulinum type A

• PDB DOI: https://doi.org/10.2210/pdb1YBI/pdb

• Classification: TOXIN
• Organism(s): Clostridium botulinum
• Mutation(s): No 


• Deposited: 2004-12-20 Released: 2005-02-22 
• Deposition Author(s): Arndt, J.W., Gu, J., Jaroszewski, L., Schwarzenbacher, R., Hanson, M., Lebeda, F.J., Stevens, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.194 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

The Structure of the Neurotoxin-associated Protein HA33/A from Clostridium botulinum Suggests a Reoccurring beta-Trefoil Fold in the Progenitor Toxin Complex.

Arndt, J.W., Gu, J., Jaroszewski, L., Schwarzenbacher, R., Hanson, M.A., Lebeda, F.J., Stevens, R.C.

(2005) J Mol Biology 346: 1083-1093

• PubMed: 15701519 
• DOI: https://doi.org/10.1016/j.jmb.2004.12.039
• Primary Citation Related Structures: 
  1YBI


• PubMed Abstract: 
  

  The hemagglutinating protein HA33 from Clostridium botulinum is associated with the large botulinum neurotoxin secreted complexes and is critical in toxin protection, internalization, and possibly activation. We report the crystal structure of serotype A HA33 (HA33/A) at 1.5 A resolution that contains a unique domain organization and a carbohydrate recognition site. In addition, sequence alignments of the other toxin complex components, including the neurotoxin BoNT/A, hemagglutinating protein HA17/A, and non-toxic non-hemagglutinating protein NTNHA/A, suggests that most of the toxin complex consists of a reoccurring beta-trefoil fold.

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Organizational Affiliation: 
• Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.5 kDa 
• Atom Count: 5,241 
• Modeled Residue Count: 568 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
non-toxin haemagglutinin HA34	A, B	288	Clostridium botulinum	Mutation(s): 0
UniProt
Find proteins for Q45871 (Clostridium botulinum) Explore Q45871  Go to UniProtKB:  Q45871

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.194 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.084	α = 90
b = 146.595	β = 90
c = 35.712	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-22 
Deposition Author(s): Arndt, J.W., Gu, J., Jaroszewski, L., Schwarzenbacher, R., Hanson, M., Lebeda, F.J., Stevens, R.C.

Revision History  

• Version 1.0: 2005-02-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Refinement description