6Q55

Crystal structure of Cryptosporidium hominis CPSF3 in complex with Compound 61


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Metal-captured inhibition of pre-mRNA processing activity by CPSF3 controls Cryptosporidium infection.

Swale, C.Bougdour, A.Gnahoui-David, A.Tottey, J.Georgeault, S.Laurent, F.Palencia, A.Hakimi, M.A.

(2019) Sci Transl Med 11

  • DOI: https://doi.org/10.1126/scitranslmed.aax7161
  • Primary Citation of Related Structures:  
    6Q55, 6Q5A

  • PubMed Abstract: 

    Cryptosporidium is an intestinal pathogen that causes severe but self-limiting diarrhea in healthy humans, yet it can turn into a life-threatening, unrelenting infection in immunocompromised patients and young children. Severe diarrhea is recognized as the leading cause of mortality for children below 5 years of age in developing countries. The only approved treatment against cryptosporidiosis, nitazoxanide, has limited efficacy in the most vulnerable patient populations, including malnourished children, and is ineffective in immunocompromised individuals. Here, we investigate inhibition of the parasitic cleavage and polyadenylation specificity factor 3 (CPSF3) as a strategy to control Cryptosporidium infection. We show that the oxaborole AN3661 selectively blocked Cryptosporidium growth in human HCT-8 cells, and oral treatment with AN3661 reduced intestinal parasite burden in both immunocompromised and neonatal mouse models of infection with greater efficacy than nitazoxanide. Furthermore, we present crystal structures of recombinantly produced Cryptosporidium CPSF3, revealing a mechanism of action whereby the mRNA processing activity of this enzyme is efficiently blocked by the binding of the oxaborole group at the metal-dependent catalytic center. Our data provide insights that may help accelerate the development of next-generation anti- Cryptosporidium therapeutics.


  • Organizational Affiliation

    Institute for Advanced Biosciences (IAB), Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, 38000 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cleavage and Polyadenylation Specificity Factor 3 (CPSF3)483Cryptosporidium hominis TU502Mutation(s): 0 
Gene Names: CHUDEA8_460
UniProt
Find proteins for A0A0S4TJL4 (Cryptosporidium hominis)
Explore A0A0S4TJL4 
Go to UniProtKB:  A0A0S4TJL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S4TJL4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HJB (Subject of Investigation/LOI)
Query on HJB

Download Ideal Coordinates CCD File 
D [auth A]3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-5-yl]propanoic acid
C10 H12 B O5
CKXGLMTUQXTCMV-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.67α = 90
b = 90.67β = 90
c = 237.59γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionFranceiNEXT Grant 653706
French National Research AgencyFranceANR-11-LABX- 0024 Parafrap

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description