Macromolecule Content

• Total Structure Weight: 9109.76 
• Atom Count: 606 
• Residue Count: 27 
• Unique nucleic acid chains: 1

1BYJ

GENTAMICIN C1A A-SITE COMPLEX

• DOI: 10.2210/pdb1BYJ/pdb
• NDB: 1BYJ

• Classification: RNA


• Deposited: 1998-10-16 Released: 1999-10-29 
• Deposition Author(s): Yoshizawa, S., Fourmy, D., Puglisi, J.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 38 
• Conformers Submitted: 38 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Literature

Structural origins of gentamicin antibiotic action.

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

(1998) EMBO J. 17: 6437-6448

• PubMed: 9822590 
• DOI: 10.1093/emboj/17.22.6437


• PubMed Abstract: 
  

Aminoglycoside antibiotics that bind to the ribosomal A site cause misreading of the genetic code and inhibit translocation. The clinically important aminoglycoside, gentamicin C, is a mixture of three components. Binding of each gentamicin component to the ribosome and to a model RNA oligonucleotide was studied biochemically and the structure of the RNA complexed to gentamicin C1a was solved using magnetic resonance nuclear spectroscopy. Gentamicin C1a binds in the major groove of the RNA. Rings I and II of gentamicin direct specific RNA-drug interactions. Ring III of gentamicin, which distinguishes this subclass of aminoglycosides, also directs specific RNA interactions with conserved base pairs. The structure leads to a general model for specific ribosome recognition by aminoglycoside antibiotics and a possible mechanism for translational inhibition and miscoding. This study provides a structural rationale for chemical synthesis of novel aminoglycosides.

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Organizational Affiliation: 

Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5400, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
RNA (16S RNA)	A	27	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GE1	A	3,4-DIDEOXY-2,6-AMINO-ALPHA-D GALACTOPYRANOSE C6 H14 N2 O2 FGFITZOBEYBNGG-JKUQZMGJSA-N
GE2	A	3,5-DIAMINO-CYCLOHEXANOL C6 H14 N2 O ORKQZIAHTZABIG-FPFOFBBKSA-N
GE3	A	5-METHYL-4-METHYLAMINO-TETRAHYDRO-PYRAN-2,3,5-TRIOL C7 H15 N O4 VXWORWYFOFDZLY-JWXFUTCRSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GE1	Kd: 2000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 38 
• Conformers Submitted: 38 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-10-16 
• Released Date: 1999-10-29 
• Deposition Author(s): Yoshizawa, S., Fourmy, D., Puglisi, J.D.

Revision History 

• Version 1.0: 1999-10-29
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance