6Q5A | pdb_00006q5a

Crystal structure of Cryptosporidium hominis CPSF3 in the apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.179 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.138 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.140 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6Q5A

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 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.

Macromolecule Content 

  • Total Structure Weight: 54.72 kDa 
  • Atom Count: 4,245 
  • Modeled Residue Count: 461 
  • Deposited Residue Count: 483 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cleavage and Polyadenylation Specificity Factor 3483Cryptosporidium hominisMutation(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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
J [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [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
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
I [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.179 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.138 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.140 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.36α = 90
b = 90.36β = 90
c = 238.66γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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