Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.67 kDa 
• Atom Count: 573 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

1FYO

EUKARYOTIC DECODING REGION A-SITE RNA

• PDB DOI: 10.2210/pdb1FYO/pdb
• NDB: 1FYO

• Classification: RNA
• Mutation(s): No 


• Deposited: 2000-10-02 Released: 2001-03-14 
• Deposition Author(s): Lynch, S.R., Puglisi, J.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 25 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Literature

Structure of a eukaryotic decoding region A-site RNA.

Lynch, S.R., Puglisi, J.D.

(2001) J Mol Biol 306: 1023-1035

• PubMed: 11237616 
• DOI: 10.1006/jmbi.2000.4419
• Primary Citation of Related Structures:  
  1FYO


• PubMed Abstract: 
  

The aminoglycoside antibiotics target a region of highly conserved nucleotides in the aminoacyl-tRNA site (A site) of 16 S RNA on the 30 S subunit. The structures of a prokaryotic decoding region A-site oligonucleotide free in solution and bound to the aminoglycosides paromomycin and gentamicin C1A have been determined. Here, the structure of a eukaryotic decoding region A-site oligonucleotide has been determined using homonuclear and heteronuclear NMR spectroscopy, and compared to the unbound prokaryotic rRNA structure. The two structures are similar, with a U1406-U1495 base-pair, a C1407-G1494 Watson-Crick base-pair, and a G1408-A1493 base-pair instead of the A1408-A1493 base-pair of the prokaryotic structure. The two structures differ in the orientation of the 1408 position with respect to A1493; G1408 is rotated toward the major groove, which is the binding pocket for aminoglycosides. The structures also differ in the stacking geometry of G1494 on A1493, which could have slight long-range conformational effects.

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Organizational Affiliation: 

Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
FRAGMENT OF 18S RIBOSOMAL RNA	A	27	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 25 
• Selection Criteria: structures with the least restraint violations,structures with the lowest energy 
• OLDERADO: 1FYO Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-10-02 
• Released Date: 2001-03-14 
Deposition Author(s): Lynch, S.R., Puglisi, J.D.

Revision History  

• Version 1.0: 2001-03-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations