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PDBsum entry 3zry
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483 a.a.
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471 a.a.
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266 a.a.
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119 a.a.
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49 a.a.
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(+ 4 more)
73 a.a.
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References listed in PDB file
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Key reference
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Title
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Rotor architecture in the yeast and bovine f1-C-Ring complexes of f-Atp synthase.
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Authors
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M.F.Giraud,
P.Paumard,
C.Sanchez,
D.Brèthes,
J.Velours,
A.Dautant.
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Ref.
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J Struct Biol, 2012,
177,
490-497.
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PubMed id
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Abstract
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The F(1)F(O)-ATP synthase is a rotary molecular nanomotor. F(1) is a chemical
motor driven by ATP hydrolysis while F(O) is an electrical motor driven by the
proton flow. The two stepping motors are mechanically coupled through a common
rotary shaft. Up to now, the three available crystal structures of the F(1)c(10)
sub-complex of the yeast F(1)F(O)-ATP synthase were isomorphous and then named
yF(1)c(10)(I). In this crystal form, significant interactions of the c(10)-ring
with the F(1)-head of neighboring molecules affected the overall conformation of
the F(1)-c-ring complex. The symmetry axis of the F(1)-head and the inertia axis
of the c-ring were tilted near the interface between the F(1)-central stalk and
the c-ring rotor, resulting in an unbalanced machine. We have solved a new
crystal form of the F(1)c(10) complex, named yF(1)c(10)(II), inhibited by
adenylyl-imidodiphosphate (AMP-PNP) and dicyclohexylcarbodiimide (DCCD), at
6.5Å resolution in which the crystal packing has a weaker influence over the
conformation of the F(1)-c-ring complex. yF(1)c(10)(II) provides a model of a
more efficient generator. yF(1)c(10)(II) and bovine bF(1)c(8) structures share a
common rotor architecture with the inertia center of the F(1)-stator close to
the rotor axis.
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Secondary reference #1
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Title
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Crystal structure of the mg·ADP-Inhibited state of the yeast f1c10-Atp synthase.
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Authors
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A.Dautant,
J.Velours,
M.F.Giraud.
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Ref.
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J Biol Chem, 2010,
285,
29502-29510.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Hydrogenated and fluorinated surfactants derived from tris(hydroxymethyl)-Acrylamidomethane allow the purification of a highly active yeast f1-F0 ATP-Synthase with an enhanced stability.
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Authors
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J.C.Talbot,
A.Dautant,
A.Polidori,
B.Pucci,
T.Cohen-Bouhacina,
A.Maali,
B.Salin,
D.Brèthes,
J.Velours,
M.F.Giraud.
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Ref.
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J Bioenerg Biomembr, 2009,
41,
349-360.
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PubMed id
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Secondary reference #3
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Title
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Molecular architecture of the rotary motor in ATP synthase.
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Authors
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D.Stock,
A.G.Leslie,
J.E.Walker.
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Ref.
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Science, 1999,
286,
1700-1705.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. Stereo views of an electron density map of the yeast
F[1]c[10] complex. The solvent flattened map was calculated at
3.9 Å resolution and contoured at 1.5  . (A) Side
view containing the bovine F[1] C  model
(with in
orange,  in yellow,
and  in
green). The density of symmetry-related molecules in the crystal
is masked out. The inset indicates the location of the subunits
within the complex. The location of the section shown in (C) is
indicated by the white box; the direction of the view is
indicated by the arrow. The presumed membrane region (M) (2) is
marked by the two dotted lines. The c subunits are numbered 3,
2, 1, 10, and 9 (the best ordered c subunit was chosen as
number 1). The overall height of the complex is ~190 Å, of
which the [3] [3]
subcomplex accounts for 83 Å, the stalk for 50 Å,
and the c subunits for 58 Å. (B) Enlarged view of the  / -c contact
region with the model (and numbering) of the E. coli  subunit
(in red) and the E. coli c subunit (in white) fitted into the
density, contoured at 1.0 . The
white box in the inset indicates the location of the displayed
section within the complex. (C) End-on view of the density of
the c ring. The inset shows the location of the , , , and subunits
in relation to the c subunits. The helices of the c subunit are
drawn as blue circles, the larger outer circles accounting for
the larger side chains in the COOH-terminal helix. The outer
diameter of the c ring is 55 Å (top) to 42 Å
(equator) to 45 Å (bottom), and the inner diameter is 27
Å (top) to 17 Å (equator) to 22 Å (bottom).
The dimensions exclude consideration of unresolved regions of
density, including amino acid side chains and detergent or lipid
molecules. The two regions of density near subunit 10 are not
extensive and are likely to be noise.
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Figure 3.
Fig. 3. Stereo view of the crystal packing of the yeast
F[1]c[10] complex. A 45 Å thick section through the
crystal perpendicular to the crystallographic y axis is shown.
The electron density is contoured at 1.2 . The red
lines mark the x and z axes of the crystal lattice. All figures
were prepared with the program MAIN (72).
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The above figures are
reproduced from the cited reference
with permission from the AAAs
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Secondary reference #4
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Title
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Novel features of the rotary catalytic mechanism revealed in the structure of yeast f1 atpase.
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Authors
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V.Kabaleeswaran,
N.Puri,
J.E.Walker,
A.G.Leslie,
D.M.Mueller.
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Ref.
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EMBO J, 2006,
25,
5433-5442.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3 Phosphate-binding site in the  [E]-subunit
of the yF[1]II complex. (A) Electron density of the final
2F[o]-F[c] map for the phosphate-binding site (contoured at 1.3
 ).
The electron density is shown only for a radius about the
phosphate to simplify the image. (B) Side chains that contribute
to phosphate binding. Possible ionic interactions are shown as
dotted lines, with distances in Å. (C) Superposition of
the phosphate-binding region of yF[1]I (green) on that of
yF[1]II (blue). (D) Superposition of the phosphate-binding
region of the empty subunit of bovine F[1] (pink) on yF[1]II
(blue). The bovine residue numbering is used in this image.
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Figure 5.
Figure 5 Relative movement of the phosphate molecule during the
catalytic cycle. The predicted path of the phosphate molecule
during catalysis is marked by the position of phosphate (or
sulfate) in the [E]-subunits
of the yF[1]II complex (blue), the bovine AlF[4]^-:ADP-inhibited
structure (Menz et al, 2001) (yellow), and the  -phosphate
of AMPPNP bound to the [DP]-subunit
of the yF[1]I complex (salmon). The structures were superimposed
using the P-loop and neighboring catalytic residues ( 151–177,
330–336).
The  -carbon
trace of the P-loop of all three enzymes is shown along with the
bound nucleotide and phosphate (or sulfate) of yF[1]II (yellow).
The inset shows just the movement of the phosphate relative to
the nucleotide. The phosphate bound to [E]
(blue) moves to the position in the AlF[4]^-:ADP-inhibited state
(yellow) and ends as the -phosphate
of ATP in the DP site (as colored). Also shown is the movement
of Arg375
in the same path. The distances between the atoms are shown in
Å.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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