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PDBsum entry 2wpd
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485 a.a.
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470 a.a.
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269 a.a.
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132 a.a.
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59 a.a.
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(+ 4 more)
76 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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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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Abstract
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The F(1)c(10) sub-complex of the yeast F(1)F(0)-ATP synthase includes the
membrane rotor part c(10)-ring linked to a catalytic head (alpha/beta)(3) by a
central stalk (gammadeltaepsilon). The Saccharomyces cerevisiae yF(1)c(10):ADP
sub-complex was crystallized in the presence of Mg.ADP, dicyclohexylcarbodiimide
(DCCD) and azide. The structure was solved by molecular replacement using a high
resolution model of the yeast F(1) and a bacterial c-ring model with 10 copies
of the c-subunit. The structure refined to 3.43 A resolution displays new
features compared to the original yF(1)c(10) and to the yF(1) inhibited by
adenylyl-imidodiphosphate (AMP-PNP) (yF(1)(I-III)). An ADP molecule was bound in
both beta(DP) and beta(TP) catalytic sites. The alpha(DP)-beta (DP) pair is
slightly open and resembles the novel conformation identified in yF(1) whereas
the alpha (TP)-beta(TP) pair is very closed and resembles more a DP pair.
yF(1)c(10) provides a model of a new Mg.ADP-inhibited state of the yeast F(1).
Like for the original yF(1) and yF(1)c(10):ADP structures, the foot of the
central stalk is rotated by about 40 degrees with respect to bovine structures.
The assembly of the F(1) central stalk with the F(0) c-ring rotor is mainly
provided by electrostatic interactions. On the rotor ring, the essential
cGlu(59) carboxylate group is surrounded by hydrophobic residues and is not
involved in hydrogen bonding.
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Secondary reference #1
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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 #2
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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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Secondary reference #3
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Title
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Asymmetric structure of the yeast f1 atpase in the absence of bound nucleotides.
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Authors
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V.Kabaleeswaran,
H.Shen,
J.Symersky,
J.E.Walker,
A.G.Leslie,
D.M.Mueller.
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Ref.
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J Biol Chem, 2009,
284,
10546-10551.
[DOI no: ]
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PubMed id
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Figure 1.
Electron density at the catalytic sites of yeast F[1] ATPase
in the absence of nucleotides. In each panel, the 2F[o] - F[c]
map is shown (contoured at 1 σ) with the position of the
nucleotide modeled from the ground state structure. The inset
plots show the region where the nucleotide would bind and
corresponding electron density. The main chain is represented as
a ribbon in red and blue for the α and β subunits,
respectively. The side chains of selected residues important for
substrate binding and catalysis are shown. A, α[DP]/β[DP]
site; B, α[TP]/β[TP] site; C, a noncatalytic (NC) site, all
for Complex I. D, the phosphate-binding site in the α[E]/β[E]
site of Complex II.
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Figure 3.
Electron density maps calculated with regions of the model
omitted. Stereo images showing the electron density omit maps
calculated excluding residues βVal-371–Leu-391 (A) and
βSer-340–Pro-350, and βGlu-422–Pro-428 (B) along with the
pertinent regions of the final model are shown. The 2F[o] - F[c]
maps are contoured at 1 σ.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #4
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Title
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Structure of the rotor ring of f-Type na+-Atpase from ilyobacter tartaricus.
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Authors
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T.Meier,
P.Polzer,
K.Diederichs,
W.Welte,
P.Dimroth.
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Ref.
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Science, 2005,
308,
659-662.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Structure of the I. tartaricus c[11] ring in ribbon
representation. Subunits are shown in different colors. (A) View
perpendicular to the membrane from the cytoplasmic side. Two
subunits are labeled. (B) Side view. The blue spheres represent
the bound Na^+ ions. Detergent molecules inside the ring are
shown with red and gray spheres for clarity. The membrane is
indicated as a gray shaded bar (width, 35 Å). The images
were created with PyMOL (36).
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Figure 2.
Fig. 2. Section of the c ring showing the interface between the
N-terminal and two C-terminal helices with those side chains
discussed in the text. This three-helix bundle represents a
functional unit responsible for Na^+ binding and allowing access
of the ion to the binding site. The view is normal to the
external surface of the c ring with the ring axis approximately
vertical. The color coding of the subunits is the same as in
Fig. 1A.
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The above figures are
reproduced from the cited reference
with permission from the AAAs
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Secondary reference #5
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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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