1NTB

2.9 A crystal structure of Streptomycin RNA-aptamer complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 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

  • DOI: 10.1016/s1074-5521(03)00024-3
  • Primary Citation of Related Structures:  
    1NTA, 1NTB

  • 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 internal loops, adopts a distinct cation-stabilized fold involving a series of S-shaped backbone turns anchored by canonical and noncanonical pairs and triples ...

    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
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Entity ID: 1
MoleculeChainsLengthOrganismImage
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'A 22N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C)-3'B 18N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRY
Query on SRY

Download Ideal Coordinates CCD File 
E [auth A]STREPTOMYCIN
C21 H39 N7 O12
UCSJYZPVAKXKNQ-HZYVHMACSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.634α = 90
b = 82.634β = 90
c = 49.153γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance