1DLL

The HC fragement of tetanus toxin complexed with lactose

• PDB DOI: https://doi.org/10.2210/pdb1DLL/pdb

• Classification: TOXIN
• Organism(s): Clostridium tetani
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-12-10 Released: 2000-03-24 
• Deposition Author(s): Emsley, P., Fotinou, C., Black, I., Fairweather, N.F., Charles, I.G., Watts, C., Hewitt, E., Isaacs, N.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.201 
• R-Value Observed: 0.211 

Literature

The structures of the H(C) fragment of tetanus toxin with carbohydrate subunit complexes provide insight into ganglioside binding.

Emsley, P., Fotinou, C., Black, I., Fairweather, N.F., Charles, I.G., Watts, C., Hewitt, E., Isaacs, N.W.

(2000) J Biol Chem 275: 8889-8894

• PubMed: 10722735 
• DOI: https://doi.org/10.1074/jbc.275.12.8889
• Primary Citation of Related Structures:  
  1D0H, 1DFQ, 1DIW, 1DLL


• PubMed Abstract: 
  

  The entry of tetanus neurotoxin into neuronal cells proceeds through the initial binding of the toxin to gangliosides on the cell surface. The carboxyl-terminal fragment of the heavy chain of tetanus neurotoxin contains the ganglioside-binding site, which has not yet been fully characterized. The crystal structures of native H(C) and of H(C) soaked with carbohydrates reveal a number of binding sites and provide insight into the possible mode of ganglioside binding.

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Organizational Affiliation: 

Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.19 kDa 
• Atom Count: 4,302 
• Modelled Residue Count: 441 
• Deposited Residue Count: 441 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TETANUS TOXIN	A	441	Clostridium tetani	Mutation(s): 0  EC: 3.4.24.68
UniProt
Find proteins for P04958 (Clostridium tetani (strain Massachusetts / E88)) Explore P04958  Go to UniProtKB:  P04958

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	B	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.201 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.076	α = 90
b = 70.882	β = 90
c = 122.238	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
X-GEN	data reduction
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-24 
Deposition Author(s): Emsley, P., Fotinou, C., Black, I., Fairweather, N.F., Charles, I.G., Watts, C., Hewitt, E., Isaacs, N.W.

Revision History  

• Version 1.0: 2000-03-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-07
  Changes: Data collection, Database references, Structure summary