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PDBsum entry 2f8k
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RNA binding protein/ RNA
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PDB id
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2f8k
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References listed in PDB file
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Key reference
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Title
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Sequence-Specific recognition of RNA hairpins by the sam domain of vts1p.
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Authors
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T.Aviv,
Z.Lin,
G.Ben-Ari,
C.A.Smibert,
F.Sicheri.
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Ref.
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Nat Struct Mol Biol, 2006,
13,
168-176.
[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
percentage match of
0%.
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Abstract
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The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator
Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that
function as sequence-specific RNA-binding domains. Here we report the 2.0-A
X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand.
Specificity of RNA binding arises from the association of a guanosine loop base
with a shallow pocket on the SAM domain and from multiple SAM domain contacts to
the unique backbone structure of the loop, defined in part by a nonplanar base
pair within the loop. We have validated NNF1 as an endogenous target of Vts1p
among 79 transcripts that copurify with Vts1p. Bioinformatic analysis of these
mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably
more stringent than that of the isolated SAM domain in vitro.
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Figure 2.
Figure 2. The SRE pentaloop structure exhibits similarity to the
UNCG and SECIS loops. (a) Stereo diagram of the SRE
pentaloop. Dashed lines indicate hydrogen bonds. (b,c) Stereo
diagrams of the SRE crystal structure overlaid with the UNCG (b,
green; PDB entry 1F7Y; ref. 21) and SECIS (c, blue; PDB entry
1WSU; ref. 22) RNA loops, respectively. Superpositions were
generated with Swiss-PDB viewer (http://www.expasy.org/spdbv/).
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Figure 3.
Figure 3. Features of the Vts1p-SAM–RNA binding interface.
(a) Schematic diagram of SRE recognition by Vts1p-SAM. Black
dashed lines, hydrogen bonds; green dashed lines, hydrophobic
interactions; blue background, the stem of the SRE; pink
background, the pentaloop; red circles, phosphate groups; blue
ovals, bridging water molecules. The labeled protein residues
are colored according to their originating secondary structure
elements as shown in the upper left schematic. (b) Stereo
diagram of the Vts1p-SAM–SRE binding interface centered on SRE
loop position G3. Red spheres, water molecules participating in
bridging interactions between protein and RNA; dashed lines,
hydrogen bonds involving the G3 base.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2006,
13,
168-176)
copyright 2006.
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