8GCC | pdb_00008gcc

T. cruzi topoisomerase II alpha bound to dsDNA and the covalent inhibitor CT1

• PDB DOI: https://doi.org/10.2210/pdb8GCC/pdb
• EM Map EMD-29930: EMDB EMDataResource
• NAKB: 8GCC

• Classification: ISOMERASE
• Organism(s): Trypanosoma cruzi strain CL Brener, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-03-01 Released: 2023-07-12 
• Deposition Author(s): Schenk, A., Deniston, C., Noeske, J.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cyanotriazoles are selective topoisomerase II poisons that rapidly cure trypanosome infections.

Rao, S.P.S., Gould, M.K., Noeske, J., Saldivia, M., Jumani, R.S., Ng, P.S., Rene, O., Chen, Y.L., Kaiser, M., Ritchie, R., Francisco, A.F., Johnson, N., Patra, D., Cheung, H., Deniston, C., Schenk, A.D., Cortopassi, W.A., Schmidt, R.S., Wiedemar, N., Thomas, B., Palkar, R., Ghafar, N.A., Manoharan, V., Luu, C., Gable, J.E., Wan, K.F., Myburgh, E., Mottram, J.C., Barnes, W., Walker, J., Wartchow, C., Aziz, N., Osborne, C., Wagner, J., Sarko, C., Kelly, J.M., Manjunatha, U.H., Maeser, P., Jiricek, J., Lakshminarayana, S.B., Barrett, M.P., Diagana, T.T.

(2023) Science 380: 1349-1356

• PubMed: 37384702 
• DOI: https://doi.org/10.1126/science.adh0614
• Primary Citation Related Structures: 
  8GCC


• PubMed Abstract: 
  

  Millions who live in Latin America and sub-Saharan Africa are at risk of trypanosomatid infections, which cause Chagas disease and human African trypanosomiasis (HAT). Improved HAT treatments are available, but Chagas disease therapies rely on two nitroheterocycles, which suffer from lengthy drug regimens and safety concerns that cause frequent treatment discontinuation. We performed phenotypic screening against trypanosomes and identified a class of cyanotriazoles (CTs) with potent trypanocidal activity both in vitro and in mouse models of Chagas disease and HAT. Cryo-electron microscopy approaches confirmed that CT compounds acted through selective, irreversible inhibition of trypanosomal topoisomerase II by stabilizing double-stranded DNA:enzyme cleavage complexes. These findings suggest a potential approach toward successful therapeutics for the treatment of Chagas disease.

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Organizational Affiliation: 
• Novartis Institute for Tropical Diseases, Emeryville, CA, USA.
Novartis Institutes for BioMedical Research, Emeryville, CA, USA.
Novartis Institute for Tropical Diseases, Singapore.
College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
Faculty of Science, University of Basel, Basel, Switzerland.
London School of Hygiene and Tropical Medicine, London, UK.
Novartis Institutes for BioMedical Research, San Diego, CA, USA.
Novartis Institutes for BioMedical Research, Basel, Switzerland.
York Biomedical Research Institute, Hull York Medical School, University of York, York, UK.
York Biomedical Research Institute, Department of Biology, University of York, York, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 196.65 kDa 
• Atom Count: 11,705 
• Modeled Residue Count: 1,462 
• Deposited Residue Count: 1,614 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2	A, B	779	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: Tc00.1047053508699.10 EC: 5.6.2.2
UniProt
Find proteins for Q4DE53 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DE53  Go to UniProtKB:  Q4DE53

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	C, D	28	Escherichia coli

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YWX (Subject of Investigation/LOI)	E [auth C], F [auth D]	2-{3-[(Z)-iminomethyl]-1H-1,2,4-triazol-1-yl}-1-{(3M)-3-[2-(trifluoromethyl)phenyl]-6H-pyrrolo[3,4-b]pyridin-6-yl}ethan-1-one C19 H13 F3 N6 O CZMOUVMERVDBNS-OUBWWKSTSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Schenk, A., Deniston, C., Noeske, J.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	219639/Z/19/Z
Wellcome Trust	United Kingdom	108517/Z/15/Z

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary