1PBR | pdb_00001pbr

STRUCTURE OF 16S RIBOSOMAL RNA, NMR, MINIMIZED AVERAGE STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1PBR/pdb
• NAKB: 1PBR

• Classification: RNA
• Mutation(s): No 


• Deposited: 1996-09-12 Released: 1997-09-17 
• Deposition Author(s): Fourmy, D., Recht, M.I., Blanchard, S., Puglisi, J.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic.

Fourmy, D., Recht, M.I., Blanchard, S.C., Puglisi, J.D.

(1996) Science 274: 1367-1371

• PubMed: 8910275 
• DOI: https://doi.org/10.1126/science.274.5291.1367
• Primary Citation Related Structures: 
  1PBR


• PubMed Abstract: 
  

  Aminoglycoside antibiotics that bind to 30S ribosomal A-site RNA cause misreading of the genetic code and inhibit translocation. The aminoglycoside antibiotic paromomycin binds specifically to an RNA oligonucleotide that contains the 30S subunit A site, and the solution structure of the RNA-paromomycin complex was determined by nuclear magnetic resonance spectroscopy. The antibiotic binds in the major groove of the model A-site RNA within a pocket created by an A-A base pair and a single bulged adenine. Specific interactions occur between aminoglycoside chemical groups important for antibiotic activity and conserved nucleotides in the RNA. The structure explains binding of diverse aminoglycosides to the ribosome, their specific activity against prokaryotic organisms, and various resistance mechanisms, and provides insight into ribosome function.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.31 kDa 
• Atom Count: 617 
• Modeled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S RIBOSOMAL RNA	A	27	N/A

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-beta-D-ribofuranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G38023GV GlyCosmos: G38023GV

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PA1	C [auth A]	2-amino-2-deoxy-alpha-D-glucopyranose C6 H13 N O5 MSWZFWKMSRAUBD-UKFBFLRUSA-N
CYY	D [auth A]	2-DEOXYSTREPTAMINE C6 H14 N2 O3 DTFAJAKTSMLKAT-JDCCYXBGSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-09-17 
Deposition Author(s): Fourmy, D., Recht, M.I., Blanchard, S., Puglisi, J.D.

Revision History  

• Version 1.0: 1997-09-17
  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: 2013-01-16
  Changes: Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Structure summary