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PDBsum entry 2g2m
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References listed in PDB file
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Key reference
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Title
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Three dimensional models of nb-Arc domains confering disease resistance in tomato, Arabidopsis and flax
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Authors
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R.Chattopadhyaya,
J.Basak,
A.Pal.
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Ref.
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TO BE PUBLISHED ...
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Secondary reference #1
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Title
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The caenorhabditis elegans cell death gene ced-4 encodes a novel protein and is expressed during the period of extensive programmed cell death.
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Authors
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J.Yuan,
H.R.Horvitz.
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Ref.
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Development, 1992,
116,
309-320.
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PubMed id
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Secondary reference #2
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Title
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The nb-Arc domain: a novel signalling motif shared by plant resistance gene products and regulators of cell death in animals
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Authors
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E.A.Van der biezen,
J.D.G.Jones.
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Ref.
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curr biol, 1998,
8,
.
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Secondary reference #3
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Title
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Structure of the apoptotic protease-Activating factor 1 bound to ADP.
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Authors
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S.J.Riedl,
W.Li,
Y.Chao,
R.Schwarzenbacher,
Y.Shi.
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Ref.
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Nature, 2005,
434,
926-933.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1: Overall structure of the WD40-deleted Apaf-1 bound to
ADP. a, A ribbon diagram of the structure of Apaf-1 (residues
1 -591) bound to ADP. Apaf-1 sequentially comprises five
distinct domains: CARD (coloured green), an  /
 fold
(blue), helical domain I (cyan), a winged-helix domain (magenta)
and helical domain II (red). These five domains pack against one
another to generate a relatively compact structure. ADP binds to
the hinge region between the /
fold
and helical domain I but is also coordinated by two critical
residues from the winged-helix domain. b, The structure of
Apaf-1 in another orientation. Relative to a, Apaf-1 is rotated
90° along a vertical axis within the plane of paper. c, A stereo
view showing the binding of ADP in the Apaf-1 structure. The
|F[o] - F[c]| omit electron density map, contoured at 2.0  ,
is calculated with the omission of ADP and shown in red around
ADP. Figures 1 -3 and 5 were prepared using MOLSCRIPT29 and
GRASP30.
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Figure 3.
Figure 3: ADP serves as an organizing centre for the adjoining
three domains and locks Apaf-1 in an inactive conformation.
a, ADP is deeply buried and inaccessible to even small molecules
unless the surrounding domains undergo conformational changes.
Left, a cross-section of Apaf-1, with its van der Waals surface
represented by a colour-coded mesh. Right, the CARD domain
(green) blocks the only solvent channel to the ADP-binding
pocket. b, A stereo representation of the coordination of ADP by
residues from three domains. As in other AAA + ATPases16, ADP is
bound primarily in the hinge region between the /
fold
(blue) and helical domain I (cyan). In Apaf-1, the winged-helix
domain also contributes a direct hydrogen bond (from His 438) to
the -phosphate
group and a water-mediated hydrogen bond (from Ser 422) to the
ribose.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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Secondary reference #4
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Title
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Development of yellow mosaic virus (ymv) resistance linked DNA marker in vigna mungo from populations segregating for ymv-Reaction
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Authors
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J.Basak,
S.Kundagrami,
T.K.Ghose,
A.Pal.
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Ref.
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mol breed, 2004,
14,
375.
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