4ZC7

Paromomycin bound to a leishmanial ribosomal A-site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural basis for selective targeting of leishmanial ribosomes: aminoglycoside derivatives as promising therapeutics.

Shalev, M.Rozenberg, H.Smolkin, B.Nasereddin, A.Kopelyanskiy, D.Belakhov, V.Schrepfer, T.Schacht, J.Jaffe, C.L.Adir, N.Baasov, T.

(2015) Nucleic Acids Res 43: 8601-8613

  • DOI: https://doi.org/10.1093/nar/gkv821
  • Primary Citation of Related Structures:  
    4ZC7

  • PubMed Abstract: 

    Leishmaniasis comprises an array of diseases caused by pathogenic species of Leishmania, resulting in a spectrum of mild to life-threatening pathologies. Currently available therapies for leishmaniasis include a limited selection of drugs. This coupled with the rather fast emergence of parasite resistance, presents a dire public health concern. Paromomycin (PAR), a broad-spectrum aminoglycoside antibiotic, has been shown in recent years to be highly efficient in treating visceral leishmaniasis (VL)-the life-threatening form of the disease. While much focus has been given to exploration of PAR activities in bacteria, its mechanism of action in Leishmania has received relatively little scrutiny and has yet to be fully deciphered. In the present study we present an X-ray structure of PAR bound to rRNA model mimicking its leishmanial binding target, the ribosomal A-site. We also evaluate PAR inhibitory actions on leishmanial growth and ribosome function, as well as effects on auditory sensory cells, by comparing several structurally related natural and synthetic aminoglycoside derivatives. The results provide insights into the structural elements important for aminoglycoside inhibitory activities and selectivity for leishmanial cytosolic ribosomes, highlighting a novel synthetic derivative, compound 3: , as a prospective therapeutic candidate for the treatment of VL.


  • Organizational Affiliation

    Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA duplex
A, B, C, D
92synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.191 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.69α = 78.92
b = 57.18β = 109.44
c = 47.7γ = 123.61
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States1 R01 GM094792-01 A1
GIFGermanyG-1048-95.5/2009

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2017-10-11
    Changes: Data collection
  • Version 1.3: 2018-01-31
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary