5N0B

Crystal structure of the tetanus neurotoxin in complex with GD1a

• PDB DOI: https://doi.org/10.2210/pdb5N0B/pdb

• Classification: TOXIN
• Organism(s): Clostridium tetani
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-02-02 Released: 2017-06-21 
• Deposition Author(s): Masuyer, G., Conrad, J., Stenmark, P.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.247 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 154.37 kDa 
• Atom Count: 10,580 
• Modelled Residue Count: 1,280 
• Deposited Residue Count: 1,335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetanus toxin	A	1,335	Clostridium tetani	Mutation(s): 2  Gene Names: tetX, CTC_p60 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
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	6		N/A
Glycosylation Resources
GlyTouCan:  G46677TE GlyCosmos:  G46677TE GlyGen:  G46677TE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.247 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.695	α = 90
b = 136.84	β = 90.07
c = 92.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Masuyer, G., Conrad, J., Stenmark, P.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2014-5667

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references
• Version 1.2: 2017-08-09
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary