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PDBsum entry 1wpe
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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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Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues.
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Authors
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C.Toyoshima,
H.Nomura,
T.Tsuda.
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Ref.
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Nature, 2004,
432,
361-368.
[DOI no: ]
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PubMed id
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Abstract
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P-type ion transporting ATPases are ATP-powered ion pumps that establish ion
concentration gradients across biological membranes. Transfer of bound cations
to the lumenal or extracellular side occurs while the ATPase is phosphorylated.
Here we report at 2.3 A resolution the structure of the calcium-ATPase of
skeletal muscle sarcoplasmic reticulum, a representative P-type ATPase that is
crystallized in the absence of Ca2+ but in the presence of magnesium fluoride, a
stable phosphate analogue. This and other crystal structures determined
previously provide atomic models for all four principal states in the reaction
cycle. These structures show that the three cytoplasmic domains rearrange to
move six out of ten transmembrane helices, thereby changing the affinity of the
Ca2+-binding sites and the gating of the ion pathway. Release of ADP triggers
the opening of the lumenal gate and release of phosphate its closure, effected
mainly through movement of the A-domain, the actuator of transmembrane gates.
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Figure 5.
Figure 5: Details of the phosphorylation site in E2
[glyph.gif] MgF[4]^2-.
In the enlarged view (b), the atomic model of
aspartylphosphate taken unchanged from a related protein CheY
(PDB accession code 1QMP)29 is incorporated. The blue net in a
shows an omit annealed Fo -Fc map (at 5  ;
temperature factor also refined) at 2.3 Å resolution. Small
spheres represent water molecules (red) and Mg2+ (green).
MgF[4]^2- is shown in ball-and-stick representation. Large
yellow arrow indicates the expected water attack to the
aspartylphosphate (P-D351). Conserved sequence motifs are shown
in a. Broken lines in pink indicate likely hydrogen bonds, and
those in light green coordinations of Mg2+.
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Figure 6.
Figure 6: A cartoon depicting the structural changes of the
Ca^2+-ATPase during the reaction cycle, based on the crystal
structures in five different states.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2004,
432,
361-368)
copyright 2004.
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Secondary reference #1
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Title
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Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 a resolution.
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Authors
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C.Toyoshima,
M.Nakasako,
H.Nomura,
H.Ogawa.
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Ref.
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Nature, 2000,
405,
647-655.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2: Architecture of the sarcoplasmic reticulum
Ca^2+-ATPase. alpha- -Helices
are represented by cylinders and beta- -strands
by arrows, as recognized by DSSP46. Cylinders are not used
for one-turn helices. Colour changes gradually from the N
terminus (blue) to the C terminus (red). Three cytoplasmic
domains are labelled (A, N and P). Transmembrane helices
(M1-M10) and those in domains A and P are numbered. The model is
orientated so that transmembrane helix M5 is parallel to the
plane of the paper. The model in the right panel is rotated by
50° around M5. The M5 helix is 60 Å long and serves as a scale.
Several key residues are shown in ball-and-stick, and TNP-AMP by
CPK. D351 is the residue of phosphorylation. Two purple spheres
represent Ca^2+ in the transmembrane binding sites. The binding
sites for phospholamban (PLN)16 and thapsigargin (TG)17 are
marked, as are major digestion sites for trypsin5 (T1 and T2)
and proteinase K28 (PrtK). The arrow specifies the direction of
view in Fig. 6b. Figure prepared with MOLSCRIPT47.
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Figure 4.
Figure 4: Details of the transmembrane Ca^2+-binding sites.
The refined model is superimposed with a 2|F[o]| - |F[c]|
composite-omit map prepared with CNS (blue meshes, contoured at
1.5 ).
The meshes in pink show omit |F[ o]| - |F[c]| map for Ca^2+ and
a bound water (cut-off at 3 ).
Blue spheres represent Ca^ 2+, and red spheres water molecules.
Viewed roughly normal to the membrane from the cytoplasmic side
(a) and parallel to the membrane (b) in stereo. The
coordinations of oxygen atoms to Ca^2+ are indicated by white
dotted lines, and possible hydrogen bonds stabilizing the
coordination geometry by green dashed lines. The viewing
direction in b is also specified in Fig. 3a. Water molecule
nearest to the Ca^ 2+-binding site is marked (asterisk). Note
the unwinding of helices M4 and M6 and rows of exposed carbonyl
oxygen atoms along these helices in b.
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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 #2
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Title
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Structural changes in the calcium pump accompanying the dissociation of calcium.
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Authors
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C.Toyoshima,
H.Nomura.
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Ref.
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Nature, 2002,
418,
605-611.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3: Interface between the transmembrane helices (M3 -M5)
and the P domain of Ca^2+-ATPase. Superimposition of the
Ca^2+-bound (E1Ca^2+, violet) and thapsigargin-bound (E2(TG),
light green) forms fitted with the P domain. The residues (in
atom colour) represent those in E2(TG). Links between the P1 and
M3 helices involve hydrogen bonds between E340 and NH of L249
(not seen) as well as OH of T247 near the top of M3. Also see
Supplementary Information Animation 3.
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Figure 5.
Figure 5: Conformation changes around the Ca^2+-binding sites.
a, C  trace
and the side chains of the coordinating residues in E1Ca^2+. b,
Composite omit map37 (at 1.2 )
and the model for the corresponding area in E2(TG). c, Stereo
view of the composite of the models for E1Ca^2+ (violet) and
E2(TG) (atom colour). The viewing direction is approximately
down the M5 helix in E1Ca^2+. Two bound Ca^2+ appear as cyan
spheres (a) or circles (c). Dashed lines in b show potential
hydrogen bonds. Orange arrows in c show the movements of the
corresponding residues during the change from E1Ca^2+ to E2(TG).
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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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Crystal structure of the calcium pump with a bound ATP analogue.
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Authors
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C.Toyoshima,
T.Mizutani.
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Ref.
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Nature, 2004,
430,
529-535.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3: Transmembrane Ca^2+-binding sites (I and II) and the
movement of the M1 helix.
a, E1  2Ca^2+;
b, E1 AMPPCP;
c, superimposition of E1 2Ca^2+
(violet) and E1 AMPPCP
(atom colour) in stereo view. Cyan (a–c) and violet spheres
(c) represent bound Ca^2+; red spheres indicate water molecules
in the crystals. Owing to the resolution limitation of the
diffraction data, no water molecules are shown in b. Dotted
lines in c show the coordination of Ca^2+ and hydrogen bonds
involving E309 and D800 side chains.
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Figure 4.
Figure 4: Omit-annealed F[o] - F[c] map around AMPPCP at 5
sigma- (a)
and the hydrogen-bonding network around AMPPCP (b). AMPPCP is
shown in ball-and-stick representation; the N- and P-domains are
coloured light green and orange, respectively. Light-green
broken lines in b show likely hydrogen bonds. A part of the
N-domain is removed for clarity. Small spheres represent Mg^2+
(green) and two water molecules (red), which coordinate to the
Mg^2+, together with  -phosphate,
carboxyl groups of Asp 351 and Asp703, and a carbonyl group of
Thr 353 (orange broken lines in a and dark-green lines in b).
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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