4EN9

Crystal structure of HA70 (HA3) subcomponent of Clostridium botulinum type C progenitor toxin in complex with alpha 2-6-sialyllactosamine

PDB DOI: https://doi.org/10.2210/pdb4EN9/pdb

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

Deposited: 2012-04-12 Released: 2012-06-06
Deposition Author(s): Yamashita, S., Yoshida, H., Tonozuka, T., Nishikawa, A., Kamitori, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.220
R-Value Work: 0.193
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Carbohydrate recognition mechanism of HA70 from Clostridium botulinum deduced from X-ray structures in complexes with sialylated oligosaccharides

Yamashita, S., Yoshida, H., Uchiyama, N., Nakakita, Y., Nakakita, S., Tonozuka, T., Oguma, K., Nishikawa, A., Kamitori, S.

(2012) FEBS Lett 586: 2404-2410

PubMed: 22684008 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2012.05.055
Primary Citation of Related Structures:
4EN6, 4EN7, 4EN8, 4EN9

PubMed Abstract:
Clostridium botulinum produces the botulinum neurotoxin, forming a large complex as progenitor toxins in association with non-toxic non-hemagglutinin and/or several different hemagglutinin (HA) subcomponents, HA33, HA17 and HA70, which bind to carbohydrate of glycoproteins from epithelial cells in the infection process. To elucidate the carbohydrate recognition mechanism of HA70, X-ray structures of HA70 from type C toxin (HA70/C) in complexes with sialylated oligosaccharides were determined, and a binding assay by the glycoconjugate microarray was performed. These results suggested that HA70/C can recognize both α2-3- and α2-6-sialylated oligosaccharides, and that it has a higher affinity for α2-3-sialylated oligosaccharides.

Organizational Affiliation

Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Kita-gun, Kagawa 761-0793, Japan.

Macromolecule Content

Total Structure Weight: 74.65 kDa
Atom Count: 5,092
Modelled Residue Count: 590
Deposited Residue Count: 644
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin components HA-22/23/53	A	224	Clostridium botulinum	Mutation(s): 0 Gene Names: HA-70
UniProt
Find proteins for P46085 (Clostridium botulinum C phage) Explore P46085 Go to UniProtKB: P46085
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46085
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin components HA-22/23/53	B	420	Clostridium botulinum	Mutation(s): 0 Gene Names: HA-70
UniProt
Find proteins for P46085 (Clostridium botulinum C phage) Explore P46085 Go to UniProtKB: P46085
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46085
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046 Query on PRD_900046	C	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.220
R-Value Work: 0.193
R-Value Observed: 0.196
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.977	α = 90
b = 175.977	β = 90
c = 80.636	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2013-07-03
Changes: Database references
Version 1.2: 2016-03-16
Changes: Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary