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PDBsum entry 1cdn
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Calcium-binding protein
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PDB id
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1cdn
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References listed in PDB file
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Key reference
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Title
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Solution structure of (cd2+)1-Calbindin d9k reveals details of the stepwise structural changes along the apo--≫(ca2+)ii1--≫(ca2+)i,Ii2 binding pathway.
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Authors
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M.Akke,
S.Forsén,
W.J.Chazin.
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Ref.
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J Mol Biol, 1995,
252,
102-121.
[DOI no: ]
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PubMed id
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Abstract
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The three-dimensional solution structure of (Cd2+)1-calbindin D9k has been
determined by distance geometry, restrained molecular dynamics and relaxation
matrix calculations using experimental constraints obtained from two-dimensional
1H and 15N-1H NMR spectroscopy. The final input data consisted of 1055 NOE
distance constraints and 71 dihedral angle constraints, corresponding to 15
constraints per residue on average. The resulting ensemble of 24 structures has
no distance or dihedral angle constraints consistently violated by more than
0.07 A and 1.8 degrees, respectively. The structure is characteristic of an
EF-hand protein, with two helix-loop-helix calcium binding motifs joined by a
flexible linker, and a short anti-parallel beta-type interaction between the two
ion-binding sites. The four helices are well defined with a root mean square
deviation from the mean coordinates of 0.35 A for the backbone atoms. The
structure of the half-saturated cadmium state was compared with the previously
determined solution structures of the apo and fully calcium saturated calbindin
D9k. The comparisons were aided by introducing the ensemble averaged distance
difference matrix as a tool for analyzing differences between two ensembles of
structures. Detailed analyses of differences between the three states in
backbone and side-chain dihedral angles, hydrogen bonds, interatomic distances,
and packing of the hydrophobic core reveal the reorganization of the protein
that occurs upon ion binding. Overall, it was found that (Cd2+)1-calbindin D9k,
representing the half-saturated calcium state with an ion in site II, is
structurally more similar to the fully calcium-saturated state than the apo
state. Thus, for the binding sequence apo-->(Ca2+)II1-->(Ca2+)I,II2, the
structural changes occurring upon ion binding are most pronounced for the first
binding step, an observation that bears significantly on the molecular basis for
cooperative calcium binding in calbindin D9k.
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Figure 7.
Figure 7. The distance difference matrix visualized on the structure. The average backbone coordinates of the apo (A, B)
and (Cd
2+
)1 (C, D) ensembles with lines connecting pairs of atoms, corresponding to the DDMs shown in Figures 6A and
B, respectively. A and C show side views with the molecules oriented as in Figure 2, while B and D show top views looking
down towards the ion binding lops, with the Cd
2+
-filled site above the empty N-terminal site. The colorcoding is the same
as in Figure 6. For clarity, only significant distance differences with an absolute value larger than 2.0 Å are included, and
elements of the DDM involving residues K1-P3 have been omitted. Prepared using GRASP (Nicholls et al., 1991).
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Figure 9.
Figure 9. Comparison of the solution structures of the apo (blue), (Cd
2+
)1 (green) and (Ca
2+
)2 (red) states. A, Helix I
(P3--A15) and the side-chains of L6, I9, F10, Y13, A14 and A15. B, helix II (K25--F36) and the side-chains of L28, L31, L32
and F36. C, Helix III (T45--D54) and the side-chains of F50 and L53. D, Helix IV (F63--I73) and the side-chains of F63, F66,
V68, V70 and I73 together with F36. The structures have been oriented to facilitate viewing of specific structural
similarities/differences and only well-defined side-chains are shown. The Figures were prepared as for Figure 8.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1995,
252,
102-121)
copyright 1995.
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Secondary reference #1
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Title
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Determination of the solution structure of apo calbindin d9k by nmr spectroscopy.
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Authors
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N.J.Skelton,
J.Kördel,
W.J.Chazin.
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Ref.
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J Mol Biol, 1995,
249,
441-462.
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PubMed id
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Secondary reference #2
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Title
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High-Resolution structure of calcium-Loaded calbindin d9k.
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Authors
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J.Kördel,
N.J.Skelton,
M.Akke,
W.J.Chazin.
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Ref.
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J Mol Biol, 1993,
231,
711-734.
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PubMed id
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Secondary reference #3
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Title
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Molecular basis for co-Operativity in ca2+ binding to calbindin d9k. 1h nuclear magnetic resonance studies of (cd2+)1-Bovine calbindin d9k.
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Authors
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M.Akke,
S.Forsén,
W.J.Chazin.
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Ref.
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J Mol Biol, 1991,
220,
173-189.
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PubMed id
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