1DLL | pdb_00001dll

The HC fragement of tetanus toxin complexed with lactose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.267 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1DLL

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

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 Biological Chem 275: 8889-8894

  • DOI: https://doi.org/10.1074/jbc.275.12.8889
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom.

Macromolecule Content 

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

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TETANUS TOXIN441Clostridium tetaniMutation(s): 0 
EC: 3.4.24.68
UniProt
Find proteins for P04958 (Clostridium tetani (strain Massachusetts / E88))
Explore P04958 
Go to UniProtKB:  P04958
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04958
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G84224TW
GlyCosmos: G84224TW
GlyGen: G84224TW

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.267 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.076α = 90
b = 70.882β = 90
c = 122.238γ = 90
Software Package:
Software NamePurpose
CCP4model building
REFMACrefinement
X-GENdata reduction
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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