8R7U | pdb_00008r7u

Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii in complex with dihydro Cyclosporin A

• PDB DOI: https://doi.org/10.2210/pdb8R7U/pdb

• Classification: ISOMERASE
• Organism(s): Toxoplasma gondii, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-27 Released: 2024-10-30 
• Deposition Author(s): Jimenez-Faraco, E., Hermoso, J.A.
• Funding Organization(s): Agencia Estatal de Investigacion (AEI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.187 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Evaluating the potential of non-immunosuppressive cyclosporin analogs for targeting Toxoplasma gondii cyclophilin: Insights from structural studies.

Favretto, F., Jimenez-Faraco, E., Catucci, G., Di Matteo, A., Travaglini-Allocatelli, C., Sadeghi, S.J., Dominici, P., Hermoso, J.A., Astegno, A.

(2024) Protein Sci 33: e5157-e5157

• PubMed: 39312281 
• DOI: https://doi.org/10.1002/pro.5157
• Primary Citation Related Structures: 
  8R7S, 8R7T, 8R7U


• PubMed Abstract: 
  

  Toxoplasmosis persists as a prevalent disease, facing challenges from parasite resistance and treatment side effects. Consequently, identifying new drugs by exploring novel protein targets is essential for effective intervention. Cyclosporin A (CsA) possesses antiparasitic activity against Toxoplasma gondii, with cyclophilins identified as possible targets. However, CsA immunosuppressive nature hinders its use as an antitoxoplasmosis agent. Here, we evaluate the potential of three CsA derivatives devoid of immunosuppressive activity, namely, NIM811, Alisporivir, and dihydrocyclosporin A to target a previously characterized cyclophilin from Toxoplasma gondii (TgCyp23). We determined the X-ray crystal structures of TgCyp23 in complex with the three analogs and elucidated their binding and inhibitory properties. The high resolution of the structures revealed the precise positioning of ligands within the TgCyp23 binding site and the details of protein-ligand interactions. A comparison with the established ternary structure involving calcineurin indicates that substitutions at position 4 in CsA derivatives prevent calcineurin binding. This finding provides a molecular explanation for why CsA analogs can target Toxoplasma cyclophilins without compromising the human immune response.

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Organizational Affiliation: 
• Department of Biotechnology, University of Verona, Verona, Italy.
Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera (IQF), CSIC, Madrid, Spain.
Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
CNR Institute of Molecular Biology and Pathology, Rome, Italy.
Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.83 kDa 
• Atom Count: 3,721 
• Modeled Residue Count: 420 
• Deposited Residue Count: 448 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A [auth B], B [auth A]	213	Toxoplasma gondii	Mutation(s): 0  Gene Names: TGRH88_026260 EC: 5.2.1.8
UniProt
Find proteins for A0A7J6KAD1 (Toxoplasma gondii) Explore A0A7J6KAD1  Go to UniProtKB:  A0A7J6KAD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrocyclosporin A	C, D	11	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MLE	C, D	LEU	Methylation	C7 H15 N O2
MVA	C, D	VAL	Methylation	C6 H13 N O2
SAR	C, D	GLY	Methylation	C3 H7 N O2

Non-standard Monomers  3 Unique
ID	Chains	Type	Formula	2D Diagram
ABA	C, D	L-PEPTIDE LINKING	C4 H9 N O2
DAL	C, D	D-PEPTIDE LINKING	C3 H7 N O2
TMD	C, D	L-PEPTIDE LINKING	C10 H21 N O3

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002553	C, D	Dihydrocyclosporin A	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.187 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.346	α = 90
b = 118.109	β = 103.67
c = 47.46	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Jimenez-Faraco, E., Hermoso, J.A.

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Funding Organization	Location	Grant Number
Agencia Estatal de Investigacion (AEI)	Spain	PID2020-115331GB-I00

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release