4ZC7

Paromomycin bound to a leishmanial ribosomal A-site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.041 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1093/nar/gkv821

  • 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 coupl ...

    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 chtimor@techunix.technion.ac.il.,Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel.,Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel.,Kresge Hearing Research Institute, Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA duplexA,B,C,D92synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download SDF File 
Download CCD File 
A, C
PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.041 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.183 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 31.690α = 78.92
b = 57.180β = 109.44
c = 47.700γ = 123.61
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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