1NTA

2.9 A crystal structure of Streptomycin RNA-aptamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Encapsulating Streptomycin within a small 40-mer RNA

Tereshko, V.Skripkin, E.Patel, D.J.

(2003) CHEM.BIOL. 10: 175-187

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe a 2.9 A X-ray structure of a complex between the aminocyclitol antibiotic streptomycin and an in vitro selected RNA aptamer, solved using the anomalous diffraction properties of Ba cations. The RNA aptamer, which contains two asymmetric i ...

    We describe a 2.9 A X-ray structure of a complex between the aminocyclitol antibiotic streptomycin and an in vitro selected RNA aptamer, solved using the anomalous diffraction properties of Ba cations. The RNA aptamer, which contains two asymmetric internal loops, adopts a distinct cation-stabilized fold involving a series of S-shaped backbone turns anchored by canonical and noncanonical pairs and triples. The streptomycin streptose ring is encapsulated by stacked arrays of bases from both loops at the elbow of the L-shaped RNA architecture. Specificity is defined by direct hydrogen bonds between all streptose functional groups and base edges that line the inner walls of the cylindrical binding pocket. By contrast, the majority of intermolecular interactions involve contacts to backbone phosphates in the published structure of streptomycin bound to the 16S rRNA.


    Organizational Affiliation

    Cellular Biochemistry & Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP*UP*GP*CP*C)-3'A22N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C)-3'B18N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
BA
Query on BA

Download SDF File 
Download CCD File 
A, B
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
SRY
Query on SRY

Download SDF File 
Download CCD File 
A
STREPTOMYCIN
STREPTOMYCIN A
C21 H39 N7 O12
UCSJYZPVAKXKNQ-HZYVHMACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 83.097α = 90.00
b = 83.097β = 90.00
c = 49.472γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-05-10
    Type: Refinement description