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PDBsum entry 3rpb
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Endocytosis/exocytosis
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PDB id
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3rpb
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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 of the janus-Faced c2b domain of rabphilin.
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Authors
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J.Ubach,
J.García,
M.P.Nittler,
T.C.Südhof,
J.Rizo.
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Ref.
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Nat Cell Biol, 1999,
1,
106-112.
[DOI no: ]
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PubMed id
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Abstract
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C2 domains are widespread protein modules that often occur as tandem repeats in
many membrane-trafficking proteins such as synaptotagmin and rabphilin. The
first and second C2 domains (C2A and C2B, respectively) have a high degree of
homology but also specific differences. The structure of the C2A domain of
synaptotagmin I has been extensively studied but little is known about the C2B
domains. We have used NMR spectroscopy to determine the solution structure of
the C2B domain of rabphilin. The overall structure of the C2B domain is very
similar to that of other C2 domains, with a rigid beta-sandwich core and loops
at the top (where Ca2+ binds) and the bottom. Surprisingly, a relatively long
alpha-helix is inserted at the bottom of the domain and is conserved in all C2B
domains. Our results, together with the Ca(2+)-independent interactions observed
for C2B domains, indicate that these domains have a Janus-faced nature, with a
Ca(2+)-binding top surface and a Ca(2+)-independent bottom surface.
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Figure 3.
Figure 3. Solution structure of the C[2]B domain. a, Backbone
superposition of the 20 simulated annealing structures of the
C[2]B domain (residues 541 -677). N and C indicate the amino and
carboxy termini, respectively. The numbers indicate the
positions of several residues to help identify the orientation
of the molecule. b, Superposition of the 20 structures showing
only the heavy atoms of side chains in a slice of 12 Å within
the centre of the domain. c, Ribbon diagram of the C[2]B domain
in the same orientation as a and b. The  -strands
have been labelled 1 -8 and the positions of the two helices and
the Ca^2+-binding region (loops 1 -3) have also been indicated.
d, Ribbon diagram of the C[2]B domain in an orientation
approximately perpendicular to that of c, which shows how helix
2 runs parallel between the two -sheets.
The ribbon diagrams were prepared with the program Molscript49.
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Figure 6.
Figure 6. Taxonomy of C[2] domains. a, Topologies of the
different subclasses of C[2] domains that have been identified
and that we refer to as topologies IA (SytI C[ 2]A domain and
PKC- C[2]
domain), IB (rabphilin C[ 2]B domain), IIA (PLC-  1
and cPLA[2] C[2] domains) and IIB (PKC- )
(see text). For simplicity, very short  -helices
within loops of several C[2] domains have not been included in
the classification. b, Superpositions of the backbone of the
rabphilin C[2]B domain (red) with the backbone of C[2] domains
from the other three subclasses (black). The superpositions with
SytI C[2]A domain (PDB code 1RSY) and the cPLA[2] C[2] domain
(PDB code 1RLW) are shown in the same orientation as Fig. 3a -c
. The superposition with the PKC- C[2]
domain (PDB code 1BDY) is shown with helix 2 in front, as in
Fig. 3d. The positions of secondary structure elements discussed
in the text (strand 8 and helix 2) are indicated.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Cell Biol
(1999,
1,
106-112)
copyright 1999.
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