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PDBsum entry 2f8s
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RNA binding protein/RNA
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PDB id
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2f8s
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References listed in PDB file
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Key reference
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Title
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A potential protein-Rna recognition event along the risc-Loading pathway from the structure of a. Aeolicus argonaute with externally bound sirna.
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Authors
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Y.R.Yuan,
Y.Pei,
H.Y.Chen,
T.Tuschl,
D.J.Patel.
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Ref.
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Structure, 2006,
14,
1557-1565.
[DOI no: ]
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PubMed id
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Abstract
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Argonaute proteins are key components of the RNA-induced silencing complex
(RISC). They provide both architectural and catalytic functionalities associated
with small interfering RNA (siRNA) guide strand recognition and subsequent guide
strand-mediated cleavage of complementary mRNAs. We report on the 3.0 A crystal
structures of 22-mer and 26-mer siRNAs bound to Aquifex aeolicus Argonaute
(Aa-Ago), where one 2 nt 3' overhang of the siRNA inserts into a cavity
positioned on the outer surface of the PAZ-containing lobe of the bilobal Aa-Ago
architecture. The first overhang nucleotide stacks over a tyrosine ring, while
the second overhang nucleotide, together with the intervening sugar-phosphate
backbone, inserts into a preformed surface cavity. Photochemical crosslinking
studies on Aa-Ago with 5-iodoU-labeled single-stranded siRNA and siRNA duplex
provide support for this externally bound siRNA-Aa-Ago complex. The structure
and biochemical data together provide insights into a protein-RNA recognition
event potentially associated with the RISC-loading pathway.
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Figure 2.
Figure 2. Detailed Views of Specific Protein-RNA
Interactions in the Complex between 22-mer siRNA and Aa-Ago
(A) A stereoview of interactions between the 2 nt overhang at
one end of the externally bound 22-mer siRNA and the outer
surface of the PAZ-containing lobe (pink-colored N and
cyan-colored PAZ domains; green-colored L1 and yellow-colored L2
linkers) of Aa-Ago (cyan-colored in Figure 1A). The overhang
base U21 stacks on the aromatic ring of orange-colored Y119,
which is highly conserved among bacterial Agos, while the
overhang base U22 is inserted into a cavity whose walls involve
segments from α2 of the N domain, α3 from the L1 linker, and
loops from the PAZ domain. Further, A1 and U20 of the terminal
A1•U20 base pair stack on the side chain of orange-colored
R123 and the U21 base, respectively.
(B) Ribbon
representation of the outward-pointing face of the
PAZ-containing lobe of the cyan-colored Aa-Ago (Figure 1A); the
bound 2 nt 3′ overhang is shown in a stick representation. The
color coding of domains and linkers is as in (A). The bound 2 nt
overhang segment is shown in a stick representation.
(C)
Surface representation of the PAZ-containing lobe as in (B); the
bound 2 nt overhang segment is shown in space-filling
representation.
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Figure 3.
Figure 3. Crystal Structure of the Complex between 22-mer
siRNA and Aa-Ago
(A) A view of the crystal structure of the
complex between externally bound 22-mer siRNA and Aa-Ago. The
color codes of the various domains and linkers of Aa-Ago are as
follows: N domain, pink; L1 linker, green; PAZ domain, cyan; L2
linker, yellow; Mid domain, pink; PIWI domain, cyan; and PIWI
box, red. The siRNA is shown in beige, except for the 2 nt
overhang at one end, which is colored red. The backbone
phosphorus atoms are colored yellow.
(B) The view in (A)
rotated by 90° along the z axis.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2006,
14,
1557-1565)
copyright 2006.
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