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PDBsum entry 1zub
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Endocytosis/exocytosis
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PDB id
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1zub
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References listed in PDB file
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Key reference
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Title
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Solution structure of the rim1alpha pdz domain in complex with an elks1b c-Terminal peptide.
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Authors
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J.Lu,
H.Li,
Y.Wang,
T.C.Südhof,
J.Rizo.
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Ref.
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J Mol Biol, 2005,
352,
455-466.
[DOI no: ]
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PubMed id
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Abstract
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PDZ domains are widespread protein modules that commonly recognize C-terminal
sequences of target proteins and help to organize macromolecular signaling
complexes. These sequences usually bind in an extended conformation to
relatively shallow grooves formed between a beta-strand and an alpha-helix in
the corresponding PDZ domains. Because of this binding mode, many PDZ domains
recognize primarily the C-terminal and the antepenultimate side-chains of the
target protein, which commonly conform to motifs that have been categorized into
different classes. However, an increasing number of PDZ domains have been found
to exhibit unusual specificities. These include the PDZ domain of RIMs, which
are large multidomain proteins that regulate neurotransmitter release and help
to organize presynaptic active zones. The RIM PDZ domain binds to the C-terminal
sequence of ELKS with a unique specificity that involves each of the four ELKS
C-terminal residues. To elucidate the structural basis for this specificity, we
have determined the 3D structure in solution of an RIM/ELKS C-terminal peptide
complex using NMR spectroscopy. The structure shows that the RIM PDZ domain
contains an unusually deep and narrow peptide-binding groove with an exquisite
shape complementarity to the four ELKS C-terminal residues in their bound
conformation. This groove is formed, in part, by a set of side-chains that is
conserved selectively in RIM PDZ domains and that hence determines, at least in
part, their unique specificity.
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Figure 5.
Figure 5. Superpositions of ribbon diagrams of the RIM1α PDZ
domain (blue) with the piccolo PDZ domain (a) and the third PDZ
domain of PSD-95 (b) (orange). The PDB accession numbers of the
piccolo PDZ domain and the third PDZ domain of PSD-95 are 1ujd
and 1be9, respectively. The models were prepared with Pymol
(DeLano Scientific, San Carlos, CA). Figure 5. Superpositions
of ribbon diagrams of the RIM1α PDZ domain (blue) with the
piccolo PDZ domain (a) and the third PDZ domain of PSD-95 (b)
(orange). The PDB accession numbers of the piccolo PDZ domain
and the third PDZ domain of PSD-95 are 1ujd and 1be9,
respectively. The models were prepared with Pymol (DeLano
Scientific, San Carlos, CA).
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Figure 6.
Figure 6. The ELKS1bC peptide binds to a narrow and deep groove
of the RIM1α PDZ domain. (a)–(d) Surface representations of
(a) the RIM1α PDZ domain, (b) the third PDZ domain of PSD-95,
(c) the sixth PDZ of GRIP1 and (d) the PDZ domain of nNOS,
complexed with target peptides (the PDB accession numbers are
1be9, 1n7f and 1b8q for (b)–(d), respectively). The surfaces
of the PDZ domains are represented in blue, and the bound
peptides are shown as stick models with the P[0], P[−1],
P-[−2], and P[−3] residues colored pink, red, yellow and
orange, respectively. The side-chains that form the top surface
of the groove in the RIM1α PDZ domain are labeled in (a). The
models were prepared with Pymol (DeLano Scientific, San Carlos,
CA; http://pymol.sourceforge.net/). Figure 6. The ELKS1bC
peptide binds to a narrow and deep groove of the RIM1α PDZ
domain. (a)–(d) Surface representations of (a) the RIM1α PDZ
domain, (b) the third PDZ domain of PSD-95, (c) the sixth PDZ of
GRIP1 and (d) the PDZ domain of nNOS, complexed with target
peptides (the PDB accession numbers are 1be9, 1n7f and 1b8q for
(b)–(d), respectively). The surfaces of the PDZ domains are
represented in blue, and the bound peptides are shown as stick
models with the P[0], P[−1], P-[−2], and P[−3] residues
colored pink, red, yellow and orange, respectively. The
side-chains that form the top surface of the groove in the
RIM1α PDZ domain are labeled in (a). The models were prepared
with Pymol (DeLano Scientific, San Carlos, CA;
http://pymol.sourceforge.net/).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2005,
352,
455-466)
copyright 2005.
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