8R7U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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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

  • DOI: https://doi.org/10.1002/pro.5157
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Biotechnology, University of Verona, Verona, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseA [auth B],
B [auth A]
213Toxoplasma gondiiMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7J6KAD1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrocyclosporin A
C, D
11synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
ABA
Query on ABA
C, D
L-PEPTIDE LINKINGC4 H9 N O2ALA
MLE
Query on MLE
C, D
L-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
C, D
L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
C, D
PEPTIDE LINKINGC3 H7 N O2GLY
TMD
Query on TMD
C, D
L-PEPTIDE LINKINGC10 H21 N O3THR
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.346α = 90
b = 118.109β = 103.67
c = 47.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agencia Estatal de Investigacion (AEI)SpainPID2020-115331GB-I00

Revision History  (Full details and data files)

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