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PDBsum entry 1sdr
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References listed in PDB file
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Key reference
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Title
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Crystal structure of an RNA dodecamer containing the escherichia coli shine-Dalgarno sequence.
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Authors
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H.Schindelin,
M.Zhang,
R.Bald,
J.P.Fürste,
V.A.Erdmann,
U.Heinemann.
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Ref.
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J Mol Biol, 1995,
249,
595-603.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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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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Figure 1.
Figure 1. Portion of a 2Fo - Fc electron density map around a terminal base-pair calculated with the final atomic model
and contoured at 1s.
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Figure 2.
Figure 2. Stereo view of a least-squares superposition of the two independent molecules of the Shine-Dalgarno
dodecamer. Both molecules are shown in an all-bond wire representation. The view is into the minor groove of the helices.
This drawing, as well as Figures 3 and 4 were prepared using Molscript (Kraulis, 1991).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1995,
249,
595-603)
copyright 1995.
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Secondary reference #1
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Title
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A single base change in the shine-Dalgarno region of 16s rrna of escherichia coli affects translation of many proteins.
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Authors
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W.F.Jacob,
M.Santer,
A.E.Dahlberg.
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Ref.
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Proc Natl Acad Sci U S A, 1987,
84,
4757-4761.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in escherichia coli.
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Authors
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A.Hui,
H.A.De boer.
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Ref.
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Proc Natl Acad Sci U S A, 1987,
84,
4762-4766.
[DOI no: ]
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PubMed id
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Headers
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