Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.22 kDa 
• Atom Count: 1045 
• Modelled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique nucleic acid chains: 2

1SDR

CRYSTAL STRUCTURE OF AN RNA DODECAMER CONTAINING THE ESCHERICHIA COLI SHINE-DALGARNO SEQUENCE

• PDB DOI: 10.2210/pdb1SDR/pdb
• NDB: ARL062

• Classification: RNA
• Mutation(s): No 


• Deposited: 1994-12-11 Released: 1995-02-27 
• Deposition Author(s): Schindelin, H., Zhang, M., Bald, R., Fuerste, J.-P., Erdmann, V.A., Heinemann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

Crystal structure of an RNA dodecamer containing the Escherichia coli Shine-Dalgarno sequence.

Schindelin, H., Zhang, M., Bald, R., Furste, J.P., Erdmann, V.A., Heinemann, U.

(1995) J Mol Biol 249: 595-603

• PubMed: 7540215 
• DOI: 10.1006/jmbi.1995.0321
• Primary Citation of Related Structures:  
  1SDR


• PubMed Abstract: 
  

The synthetic dodecameric RNA fragment rUAAGGAGGUGAU resembles a region upstream of the initiation site in prokaryotic mRNAs whereas the pyrimidine-rich complementary strand is identical to the last 12 nucleotides of Escherichia coli 16 S rRNA. The complex thus serves as a model for the Shine-Dalgarno interaction which is required for proper initiation of translation. The crystal structure of rUAAGGAGGUGUA.rAUCACCUCCUUA has been determined at 2.6 A resolution and refined against 2957 1 sigma(F) structure amplitudes to an R-value of 0.195. The unit cell of the triclinic crystals contains two double-stranded RNA molecules. The conformation of the two duplexes is similar, with a root-mean-square deviation of 0.683 A between equivalent atoms, and resembles calf thymus A-DNA as determined by X-ray fiber diffraction methods. Both molecules from continuous helices that penetrate the entire crystal, but the dinucleotide step in between dodecameric duplexes has an unusual geometry with a negative twist angle. The long helices cross over each other in a characteristic manner by inserting the backbone of one molecule into the minor groove of another. These contacts are stabilized by several direct intermolecular hydrogen bonds most of which are mediated by 2'-hydroxyl groups of the ribose sugars suggesting a general mode for the interaction between RNA molecules which is different from DNA-DNA interactions.

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Related Citations: 

• A Single Base Change in the Shine-Dalgarno Region of 16s RRNA of Escherichia Coli Affects Translation of Many Proteins
  Jacobs, W.F., Santer, M., Dahlberg, A.E.
  (1987) Proc Natl Acad Sci U S A 84: 4757

• Specialized Ribosome Systems: Preferential Translation of a Single MRNA Species by a Subpopulation of Mutated Ribosomes in Escherichia Coli
  Hui, A., De Boer, H.A.
  (1987) Proc Natl Acad Sci U S A 84: 4762

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Organizational Affiliation: 

Forschungsgruppe Kristallographie Max-Delbrück-Centrum für Molekulare Medizin, Berlin, FRG.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*AP*AP*GP*GP*AP*GP*GP*UP*GP*AP*U)-3')	A, C	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*UP*CP*AP*CP*CP*UP*CP*CP*UP*UP*A)-3')	B, D	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.69	α = 90.92
b = 30.9	β = 103.63
c = 41.98	γ = 113.81

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-12-11 
• Released Date: 1995-02-27 
Deposition Author(s): Schindelin, H., Zhang, M., Bald, R., Fuerste, J.-P., Erdmann, V.A., Heinemann, U.

Revision History  

• Version 1.0: 1995-02-27
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance