1PBR

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


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1126/science.274.5291.1367
  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNA27N/A
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-beta-D-ribofuranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G38023GV
GlyCosmos:  G38023GV
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PA1
Query on PA1

Download Ideal Coordinates CCD File 
C [auth A]2-amino-2-deoxy-alpha-D-glucopyranose
C6 H13 N O5
MSWZFWKMSRAUBD-UKFBFLRUSA-N
CYY
Query on CYY

Download Ideal Coordinates CCD File 
D [auth A]2-DEOXYSTREPTAMINE
C6 H14 N2 O3
DTFAJAKTSMLKAT-JDCCYXBGSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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