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PDBsum entry 1e8o
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Alu ribonucleoprotein particle
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PDB id
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1e8o
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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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Structure and assembly of the alu domain of the mammalian signal recognition particle.
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Authors
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O.Weichenrieder,
K.Wild,
K.Strub,
S.Cusack.
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Ref.
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Nature, 2000,
408,
167-173.
[DOI no: ]
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PubMed id
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Abstract
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The Alu domain of the mammalian signal recognition particle (SRP) comprises the
heterodimer of proteins SRP9 and SRP14 bound to the 5' and 3' terminal sequences
of SRP RNA. It retards the ribosomal elongation of signal-peptide-containing
proteins before their engagement with the translocation machinery in the
endoplasmic reticulum. Here we report two crystal structures of the heterodimer
SRP9/14 bound either to the 5' domain or to a construct containing both 5' and
3' domains. We present a model of the complete Alu domain that is consistent
with extensive biochemical data. SRP9/14 binds strongly to the conserved core of
the 5' domain, which forms a U-turn connecting two helical stacks. Reversible
docking of the more weakly bound 3' domain might be functionally important in
the mechanism of translational regulation. The Alu domain structure is probably
conserved in other cytoplasmic ribonucleoprotein particles and retroposition
intermediates containing SRP9/14-bound RNAs transcribed from Alu repeats or
related elements in genomic DNA.
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Figure 1.
Figure 1: Mammalian SRP and Alu domain RNA constructs. a,
Mammalian SRP with SRP RNA bound to six proteins. The Alu domain
is coloured red (SRP9), green (SRP14), blue (Alu RNA 5' domain)
and cyan (Alu RNA 3' domain). b, SA86, the minimal Alu RNA
folding domain. S-domain RNA is replaced by a GUAA tetraloop
(grey). The green arrow indicates flexibility between the RNA 5'
and 3' domains. Hydroxyl-radical footprints of SRP9/14 on SRP
RNA are highlighted in magenta^21. c, SA88, a circular
permutation of SA86. The original 5' and 3' ends are connected
by a mono-uridine linker (black), constraining the RNA 5' and 3'
domains to stack in an extended conformation (red bar). The GUAA
tetraloop is replaced by a terminal stem (grey). The asymmetric
internal loop is highlighted (yellow).
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Figure 5.
Figure 5: Structure of the Alu domain of the mammalian SRP (see
Fig. 1 for colours). a, The SA88 Alu RNP with the alternative
conformation of loop L1.2 in the SA50 Alu RNP in orange and the
two europium sites in magenta. The disordered SRP14  1-
2
loop is indicated by a dotted line; helix H3.2 is coloured
yellow; H, helix; L, loop. b, The SA88 Alu RNP dimer viewed down
its crystallographic two-fold axis. c, Model for an Alu RNP
(SA86) in its fully folded, physiological conformation with
hydroxyl-radical footprints of SRP9/14 on SRP RNA^ 21 in
magenta. d, As c, viewed down the SRP9/14 -sheet
and illustrating the coverage of the previously exposed SRP9
surface with cysteines in yellow ball-and-stick representation.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2000,
408,
167-173)
copyright 2000.
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