Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.61 kDa 
• Atom Count: 575 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 2

1A3M

PAROMOMYCIN BINDING INDUCES A LOCAL CONFORMATIONAL CHANGE IN THE A SITE OF 16S RRNA, NMR, 20 STRUCTURES

• PDB DOI: 10.2210/pdb1A3M/pdb
• NDB: 1A3M

• Classification: RNA
• Mutation(s): No 


• Deposited: 1998-01-22 Released: 1998-04-29 
• Deposition Author(s): Fourmy, D., Yoshizawa, S., Puglisi, J.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 

Literature

Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA.

Fourmy, D., Yoshizawa, S., Puglisi, J.D.

(1998) J Mol Biol 277: 333-345

• PubMed: 9514734 
• DOI: 10.1006/jmbi.1997.1551
• Primary Citation of Related Structures:  
  1A3M


• PubMed Abstract: 
  

Aminoglycoside antibiotics that bind to ribosomal RNA in the aminoacyl-tRNA site (A-site) cause misreading of the genetic code and inhibit translocation. An A-site RNA oligonucleotide specifically binds to aminoglycoside antibiotics and the structure of the RNA-paromomycin complex was previously determined by nuclear magnetic resonance (NMR) spectroscopy. Here, the A-site RNA structure in its free form has been determined using heteronuclear NMR and compared to the structure of the paromomycin-RNA complex. As in the complex with paromomycin, the asymmetric internal loop is closed by a Watson-Crick base-pair (C1407.G1494) and by two non-canonical base-pairs (U1406.U1495, A1408.A1493). A1492 stacks below A1493 and is intercalated between the upper and lower stems. The comparison of the free and bound conformations of the RNA shows that two universally conserved residues of the A site of 16 S rRNA, A1492 and A1493, are displaced towards the minor groove of the RNA helix in presence of antibiotic. These changes in the RNA conformation place the N1 positions of A1492 and A1493 on the minor groove side of the A-site RNA and suggest a mechanism of action of aminoglycosides on translation.

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Organizational Affiliation: 

Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S RRNA (5'-R(*GP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*UP*UP*C)-3')	A	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
16S RRNA (5'-R(*GP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*C)-3')	B	13	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• OLDERADO: 1A3M Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-01-22 
• Released Date: 1998-04-29 
Deposition Author(s): Fourmy, D., Yoshizawa, S., Puglisi, J.D.

Revision History  

• Version 1.0: 1998-04-29
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Data collection, Database references, Derived calculations, Other