Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.17 kDa 
• Atom Count: 929 
• Modelled Residue Count: 42 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

2O3X

Crystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30

• PDB DOI: 10.2210/pdb2O3X/pdb
• NDB: DR0039

• Classification: RNA
• Mutation(s): No 


• Deposited: 2006-12-02 Released: 2007-11-06 
• Deposition Author(s): Kondo, J., Hainrichson, M., Nudelman, I., Shallom-Shezifi, D., Baasov, T., Westhof, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.285 
• R-Value Work: 0.246 

Literature

Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites.

Kondo, J., Hainrichson, M., Nudelman, I., Shallom-Shezifi, D., Barbieri, C.M., Pilch, D.S., Westhof, E., Baasov, T.

(2007) Chembiochem 8: 1700-1709

• PubMed: 17705310 
• DOI: 10.1002/cbic.200700271
• Primary Citation of Related Structures:  
  2O3V, 2O3W, 2O3X, 2O3Y


• PubMed Abstract: 
  

The lack of absolute prokaryotic selectivity of natural antibiotics is widespread and is a significant clinical problem. The use of this disadvantage of aminoglycoside antibiotics for the possible treatment of human genetic diseases is extremely challenging. Here, we have used a combination of biochemical and structural analysis to compare and contrast the molecular mechanisms of action and the structure-activity relationships of a new synthetic aminoglycoside, NB33, and a structurally similar natural aminoglycoside apramycin. The data presented herein demonstrate the general molecular principles that determine the decreased selectivity of apramycin for the prokaryotic decoding site, and the increased selectivity of NB33 for the eukaryotic decoding site. These results are therefore extremely beneficial for further research on both the design of new aminoglycoside-based antibiotics with diminished deleterious effects on humans, as well as the design of new aminoglycoside-based structures that selectively target the eukaryotic ribosome.

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Organizational Affiliation: 

Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, CNRS, 15 rue René Descartes, 67084 Strasbourg, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')	A, B	23	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N30	C [auth B]	(1R,2R,3S,4R,6S)-4,6-DIAMINO-2-[(5-AMINO-5-DEOXY-BETA-D-RIBOFURANOSYL)OXY]-3-HYDROXYCYCLOHEXYL 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE C17 H34 N4 O10 FNBQIDOUCINBIA-VVPCINPTSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N30	PDBBind:  2O3X	Kd: 5.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.285 
• R-Value Work: 0.246 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.14	α = 90
b = 46.83	β = 90
c = 85.72	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-12-02 
• Released Date: 2007-11-06 
Deposition Author(s): Kondo, J., Hainrichson, M., Nudelman, I., Shallom-Shezifi, D., Baasov, T., Westhof, E.

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance