9UG6 | pdb_00009ug6

Crystal structure of HA3 from Clostridium botulinum type B with alpha2,6-sialyllactose

PDB DOI: https://doi.org/10.2210/pdb9UG6/pdb

Classification: TOXIN
Organism(s): Clostridium botulinum B1 str. Okra
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-11 Released: 2025-11-05
Deposition Author(s): Amatsu, S., Kitadokoro, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.287 (Depositor), 0.288 (DCC)
R-Value Work:
0.229 (Depositor), 0.232 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Gut mucin fucosylation dictates the entry of botulinum toxin complexes

Amatsu, S., Matsumura, T., Morimoto, C., Keisham, S., Goto, Y., Kohda, T., Hirabayashi, J., Kitadokoro, K., Katayama, T., Kiyono, H., Tateno, H., Zuka, M., Fujinaga, Y.

To be published.

Macromolecule Content

Total Structure Weight: 216.17 kDa
Atom Count: 14,200
Modeled Residue Count: 1,751
Deposited Residue Count: 1,896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HA3	A, B, C	632	Clostridium botulinum B1 str. Okra	Mutation(s): 0 Gene Names: ha3
UniProt
Find proteins for Q33CP8 (Clostridium botulinum B) Explore Q33CP8 Go to UniProtKB: Q33CP8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q33CP8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-glucopyranose	D [auth E]	2		N/A	Interactions Focus chain D [auth E] Interactions & Density Focus chain D [auth E]
Glycosylation Resources
GlyTouCan: G89416UR GlyCosmos: G89416UR

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA (Subject of Investigation/LOI) Query on SIA Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.287 (Depositor), 0.288 (DCC)
R-Value Work: 0.229 (Depositor), 0.232 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.251	α = 90
b = 145.697	β = 90
c = 159.708	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.