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PDBsum entry 1b7f
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RNA-binding protein/RNA
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PDB id
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1b7f
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural basis for recognition of the tra mRNA precursor by the sex-Lethal protein.
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Authors
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N.Handa,
O.Nureki,
K.Kurimoto,
I.Kim,
H.Sakamoto,
Y.Shimura,
Y.Muto,
S.Yokoyama.
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Ref.
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Nature, 1999,
398,
579-585.
[DOI no: ]
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PubMed id
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Abstract
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The Sex-lethal (Sxl) protein of Drosophila melanogaster regulates alternative
splicing of the transformer (tra) messenger RNA precursor by binding to the tra
polypyrimidine tract during the sex-determination process. The crystal structure
has now been determined at 2.6 A resolution of the complex formed between two
tandemly arranged RNA-binding domains of the Sxl protein and a 12-nucleotide,
single-stranded RNA derived from the tra polypyrimidine tract. The two
RNA-binding domains have their beta-sheet platforms facing each other to form a
V-shaped cleft. The RNA is characteristically extended and bound in this cleft,
where the UGUUUUUUU sequence is specifically recognized by the protein. This
structure offers the first insight, to our knowledge, into how a protein binds
specifically to a cognate RNA without any intramolecular base-pairing.
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Figure 3.
Figure 3: Distribution of the electrostatic potential on the
solvent-accessible surface of Sxl (stereo view). The bound
12-nucleotide RNA is indicated in yellow by a ball-and-stick
representation. The V-shaped interdomain cleft and the surface
on the RBD2  -sheet
platform are strongly electropositive (blue); these accommodate
the phosphodiester backbone of the elongated RNA well. On the
other hand, electronegative regions (red) are scattered. This
figure was drawn using MOLMOL^50.
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Figure 4.
Figure 4: The U3–U11 (UGUUUUUUU) RNA segment in the complex
(stereo view). RNA is represented by a wire-loop model in
yellow, with atoms of nitrogen, oxygen and phosphorus shown in
blue, red and purple, respectively. The ribose moieties, except
for U8, are in the C2'-endo form. Light green broken lines show
the intramolecular hydrogen bonds that characterize the turn
conformation of RNA. The side chains of the amino acids that
interact with the RNA backbone are represented in green. Red
broken lines denote the intermolecular hydrogen bonds of the
amino-acid side chains with the phosphate–sugar backbone.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(1999,
398,
579-585)
copyright 1999.
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