5CY0

Total Chemical Synthesis, Covalent Structure Verification, and X-ray Structure of Bioactive Ts3 Toxin by Racemic Protein Crystallography

• PDB DOI: https://doi.org/10.2210/pdb5CY0/pdb

• Classification: TOXIN
• Organism(s): Tityus serrulatus
• Mutation(s): No 


• Deposited: 2015-07-29 Released: 2016-06-01 
• Deposition Author(s): Dang, B., Kubota, T., Mandal, K., Correa, A.M., Bezanilla, F., Kent, S.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.304 
• R-Value Work: 0.256 
• R-Value Observed: 0.259 

Literature

Elucidation of the Covalent and Tertiary Structures of Biologically Active Ts3 Toxin.

Dang, B., Kubota, T., Mandal, K., Correa, A.M., Bezanilla, F., Kent, S.B.

(2016) Angew Chem Int Ed Engl 55: 8639-8642

• PubMed: 27244051 
• DOI: https://doi.org/10.1002/anie.201603420
• Primary Citation of Related Structures:  
  5CY0


• PubMed Abstract: 
  

  Ts3 is an alpha scorpion toxin from the venom of the Brazilian scorpion Tityus serrulatus. Ts3 binds to the domain IV voltage sensor of voltage-gated sodium channels (Nav ) and slows down their fast inactivation. The covalent structure of the Ts3 toxin is uncertain, and the structure of the folded protein molecule is unknown. Herein, we report the total chemical synthesis of four candidate Ts3 toxin protein molecules and the results of structure-activity studies that enabled us to establish the covalent structure of biologically active Ts3 toxin. We also report the synthesis of the mirror image form of the Ts3 protein molecule, and the use of racemic protein crystallography to determine the folded (tertiary) structure of biologically active Ts3 toxin by X-ray diffraction.

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Organizational Affiliation: 

Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA.

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: 7.74 kDa 
• Atom Count: 598 
• Modelled Residue Count: 63 
• Deposited Residue Count: 64 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ts3 Toxin	A	64	Tityus serrulatus	Mutation(s): 0
UniProt
Find proteins for P01496 (Tityus serrulatus) Explore P01496  Go to UniProtKB:  P01496

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.304 
• R-Value Work: 0.256 
• R-Value Observed: 0.259 
• Space Group: P -1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 19.322	α = 101.17
b = 30.406	β = 91.26
c = 52.468	γ = 98.61

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Dang, B., Kubota, T., Mandal, K., Correa, A.M., Bezanilla, F., Kent, S.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54 GM087519
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01- GM030376
American Heart Association	United States	13POST14800031
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41 GM103403

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references
• Version 1.2: 2016-07-27
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2018-01-17
  Changes: Author supporting evidence
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Refinement description