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: 16.08 kDa 
• Atom Count: 1286 
• Modelled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 1

2PWT

Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group

• PDB DOI: 10.2210/pdb2PWT/pdb
• NDB: DR0040

• Classification: RNA/ANTIBIOTIC
• Mutation(s): No 


• Deposited: 2007-05-13 Released: 2007-09-18 
• Deposition Author(s): Kondo, J., Pachamuthu, K., Francois, B., Szychowski, J., Hanessian, S., Westhof, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 

Literature

Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity

Kondo, J., Pachamuthu, K., Francois, B., Szychowski, J., Hanessian, S., Westhof, E.

(2007) ChemMedChem 2: 1631-1638

• PubMed: 17722211 
• DOI: 10.1002/cmdc.200700113
• Primary Citation of Related Structures:  
  2PWT


• PubMed Abstract: 
  

The crystal structure of the complex between oligonucleotide containing the bacterial ribosomal decoding site (A site) and the synthetic paromomycin analogue 1, which contains the gamma-amino-alpha-hydroxybutyryl (L-haba) group at position N1 of ring II (2-DOS ring), and an ether chain with an O-phenethylaminoethyl group at position C2'' of ring III, is reported. Interestingly, next to the paromomycin analogue 1 specifically bound to the A site, a second molecule of 1 with a different conformation is observed at the crystal packing interface which mimics the A-minor interaction between two bulged-out adenines from the A site and the codon-anticodon stem of the mRNA-tRNA complex. Improved antibacterial activity supports the conclusion that analogue 1 might affect protein synthesis on the ribosome in two different ways: 1) specific binding to the A site forces maintenance of the "on" state with two bulged out adenines, and 2) a new binding mode of 1 to an A-minor motif which stabilizes complex formation between the ribosome and the mRNA-tRNA complex regardless of whether the codon-anticodon stem is of the cognate or near-cognate type.

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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
22-mer of the ribosomal decoding site	A, B	21	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LHA	C [auth A], D [auth B], E [auth B]	DOUBLY FUNCTIONALIZED PAROMOMYCIN PM-II-162 C37 H65 N7 O16 KITFYJSEQIOMTC-AFTVZRPJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.243 
• R-Value Work: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.49	α = 90
b = 43.02	β = 90
c = 98.75	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-13 
• Released Date: 2007-09-18 
Deposition Author(s): Kondo, J., Pachamuthu, K., Francois, B., Szychowski, J., Hanessian, S., Westhof, E.

Revision History  

• Version 1.0: 2007-09-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-09
  Changes: Database references, Derived calculations, Structure summary