5LR0 | pdb_00005lr0

Binding domain of Botulinum Neurotoxin DC in complex with SialylT

• PDB DOI: https://doi.org/10.2210/pdb5LR0/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium botulinum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-18 Released: 2017-08-30 
• Deposition Author(s): Berntsson, R.P.-A., Stenmark, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the unique ganglioside and cell membrane recognition mechanism of botulinum neurotoxin DC.

Zhang, S., Berntsson, R.P., Tepp, W.H., Tao, L., Johnson, E.A., Stenmark, P., Dong, M.

(2017) Nat Commun 8: 1637-1637

• PubMed: 29158482 
• DOI: https://doi.org/10.1038/s41467-017-01534-z
• Primary Citation Related Structures: 
  5LR0


• PubMed Abstract: 
  

  Botulinum neurotoxins (BoNTs), the most potent toxins known, are potential bioterrorism agents. It is well established that all seven serotypes of BoNTs (BoNT/A-G) require complex gangliosides as co-receptors. Here, we report that BoNT/DC, a presumed mosaic toxin between BoNT/D and BoNT/C1, binds and enters efficiently into neurons lacking complex gangliosides and shows no reduction in toxicity in mice deficient in complex gangliosides. The co-crystal structure of BoNT/DC with sialyl-Thomsen-Friedenreich antigen (Sialyl-T) suggests that BoNT/DC recognizes only the sialic acid, but not other moieties in gangliosides. Using liposome flotation assays, we demonstrate that an extended loop in BoNT/DC directly interacts with lipid membranes, and the co-occurring sialic acid binding and loop-membrane interactions mediate the recognition of gangliosides in membranes by BoNT/DC. These findings reveal a unique mechanism for cell membrane recognition and demonstrate that BoNT/DC can use a broad range of sialic acid-containing moieties as co-receptors.

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Organizational Affiliation: 
• Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA.
Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden.
Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden.
Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA.
Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden. [e-mail].
Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA. [e-mail].
Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA. [e-mail].

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: 101.5 kDa 
• Atom Count: 6,944 
• Modeled Residue Count: 819 
• Deposited Residue Count: 862 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin D/C protein	A, B	431	Clostridium botulinum	Mutation(s): 0  Gene Names: bont, boNT D, C, DC, NT EC: 3.4.24.69
UniProt
Find proteins for A5JGM8 (Clostridium botulinum) Explore A5JGM8  Go to UniProtKB:  A5JGM8

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan: G02684WR GlyCosmos: G02684WR GlyGen: G02684WR

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan: G01534TU GlyCosmos: G01534TU GlyGen: G01534TU

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	E [auth B]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.699	α = 90
b = 109.699	β = 90
c = 210.461	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Berntsson, R.P.-A., Stenmark, P.

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary