5B2H | pdb_00005b2h

Crystal structure of HA33 from Clostridium botulinum serotype C strain Yoichi

• PDB DOI: https://doi.org/10.2210/pdb5B2H/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Clostridium botulinum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-15 Released: 2016-06-15 
• Deposition Author(s): Akiyama, T., Hayashi, S., Matsumoto, T., Hasegawa, K., Yamano, A., Suzuki, T., Niwa, K., Watanabe, T., Sagane, Y., Yajima, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Conformational divergence in the HA-33/HA-17 trimer of serotype C and D botulinum toxin complex

Sagane, Y., Hayashi, S., Akiyama, T., Matsumoto, T., Hasegawa, K., Yamano, A., Suzuki, T., Niwa, K., Watanabe, T., Yajima, S.

(2016) Biochem Biophys Res Commun 476: 280-285

• PubMed: 27237978 
• DOI: https://doi.org/10.1016/j.bbrc.2016.05.113
• Primary Citation Related Structures: 
  5B2H


• PubMed Abstract: 
  

  Clostridium botulinum produces a large toxin complex (L-TC) comprising botulinum neurotoxin associated with auxiliary nontoxic proteins. A complex of 33- and 17-kDa hemagglutinins (an HA-33/HA-17 trimer) enhances L-TC transport across the intestinal epithelial cell layer via binding HA-33 to a sugar on the cell surface. At least two subtypes of serotype C/D HA-33 exhibit differing preferences for the sugars sialic acid and galactose. Here, we compared the three-dimensional structures of the galactose-binding HA-33 and HA-33/HA-17 trimers produced by the C-Yoichi strain. Comparisons of serotype C/D HA-33 sequences reveal a variable region with relatively low sequence similarity across the C. botulinum strains; the variability of this region may influence the manner of sugar-recognition by HA-33. Crystal structures of sialic acid- and galactose-binding HA-33 are broadly similar in appearance. However, small-angle X-ray scattering revealed distinct solution structures for HA-33/HA-17 trimers. A structural change in the C-terminal variable region of HA-33 might cause a dramatic shift in the conformation and sugar-recognition mode of HA-33/HA-17 trimer.

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Organizational Affiliation: 
• Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan. Electronic address: [e-mail].
Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan.
Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
Rigaku Corporation, 3-9-12 Matsubara-Cho, Akishima 196-8666, Japan.
Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.84 kDa 
• Atom Count: 4,960 
• Modeled Residue Count: 566 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HA-33	A, B	283	Clostridium botulinum	Mutation(s): 0  Gene Names: ha-33
UniProt
Find proteins for Q93HT5 (Clostridium botulinum) Explore Q93HT5  Go to UniProtKB:  Q93HT5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.517	α = 90
b = 142.517	β = 90
c = 126.794	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Akiyama, T., Hayashi, S., Matsumoto, T., Hasegawa, K., Yamano, A., Suzuki, T., Niwa, K., Watanabe, T., Sagane, Y., Yajima, S.

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2016-07-20
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description