 |
PDBsum entry 1cb1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Calcium-binding protein
|
PDB id
|
|
|
|
1cb1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Biochemistry
31:1011-1020
(1992)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Three-dimensional solution structure of Ca(2+)-loaded porcine calbindin D9k determined by nuclear magnetic resonance spectroscopy.
|
|
M.Akke,
T.Drakenberg,
W.J.Chazin.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The three-dimensional solution structure of native, intact porcine calbindin D9k
has been determined by distance geometry and restrained molecular dynamics
calculations using distance and dihedral angle constraints obtained from 1H NMR
spectroscopy. The protein has a well-defined global fold consisting of four
helices oriented in a pairwise antiparallel manner such that two pairs of
helix-loop-helix motifs (EF-hands) are joined by a linker segment. The two
EF-hands are further coupled through a short beta-type interaction between the
two Ca(2+)-binding loops. Overall, the structure is very similar to that of the
highly homologous native, minor A form of bovine calbindin D9k determined by
X-ray crystallography [Szebenyi, D. M. E., & Moffat, K. (1986) J. Biol.
Chem. 261, 8761-8776]. A model structure built from the bovine calbindin D9k
crystal structure shows several deviations larger than 2 A from the experimental
distance constraints for the porcine protein. These structural differences are
efficiently removed by subjecting the model structure to the experimental
distance and dihedral angle constraints in a restrained molecular dynamics
protocol, thereby generating a model that is very similar to the refined
distance geometry derived structures. The N-terminal residues of the intact
protein that are absent in the minor A form appear to be highly flexible and do
not influence the structure of other regions of the protein. This result is
important because it validates the conclusions drawn from the wide range of
studies that have been carried out on minor A forms rather than the intact
calbindin D9k.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
A.Passerini,
M.Punta,
A.Ceroni,
B.Rost,
and
P.Frasconi
(2006).
Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks.
|
| |
Proteins,
65,
305-316.
|
|
|
|
|
|
|
A.C.Dempsey,
M.P.Walsh,
and
G.S.Shaw
(2003).
Unmasking the annexin I interaction from the structure of Apo-S100A11.
|
| |
Structure,
11,
887-897.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.S.Brown,
R.Needleman,
and
J.K.Lanyi
(2000).
Origins of deuterium kinetic isotope effects on the proton transfers of the bacteriorhodopsin photocycle.
|
| |
Biochemistry,
39,
938-945.
|
|
|
|
|
|
|
L.Sandberg,
and
O.Edholm
(1999).
A fast and simple method to calculate protonation states in proteins.
|
| |
Proteins,
36,
474-483.
|
|
|
|
|
|
|
D.E.Brodersen,
M.Etzerodt,
P.Madsen,
J.E.Celis,
H.C.Thøgersen,
J.Nyborg,
and
M.Kjeldgaard
(1998).
EF-hands at atomic resolution: the structure of human psoriasin (S100A7) solved by MAD phasing.
|
| |
Structure,
6,
477-489.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.R.Biekofsky,
S.R.Martin,
J.P.Browne,
P.M.Bayley,
and
J.Feeney
(1998).
Ca2+ coordination to backbone carbonyl oxygen atoms in calmodulin and other EF-hand proteins: 15N chemical shifts as probes for monitoring individual-site Ca2+ coordination.
|
| |
Biochemistry,
37,
7617-7629.
|
|
|
|
|
|
|
D.Chaudhuri,
W.D.Horrocks,
J.C.Amburgey,
and
D.J.Weber
(1997).
Characterization of lanthanide ion binding to the EF-hand protein S100 beta by luminescence spectroscopy.
|
| |
Biochemistry,
36,
9674-9680.
|
|
|
|
|
|
|
B.C.Potts,
G.Carlström,
K.Okazaki,
H.Hidaka,
and
W.J.Chazin
(1996).
1H NMR assignments of apo calcyclin and comparative structural analysis with calbindin D9k and S100 beta.
|
| |
Protein Sci,
5,
2162-2174.
|
|
|
|
|
|
|
G.S.Shaw,
and
B.D.Sykes
(1996).
NMR solution structure of a synthetic troponin C heterodimeric domain.
|
| |
Biochemistry,
35,
7429-7438.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.M.Kilby,
L.J.Van Eldik,
and
G.C.Roberts
(1996).
The solution structure of the bovine S100B protein dimer in the calcium-free state.
|
| |
Structure,
4,
1041-1052.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.P.Smith,
K.R.Barber,
S.D.Dunn,
and
G.S.Shaw
(1996).
Structural influence of cation binding to recombinant human brain S100b: evidence for calcium-induced exposure of a hydrophobic surface.
|
| |
Biochemistry,
35,
8805-8814.
|
|
|
|
|
|
|
J.J.Falke,
S.K.Drake,
A.L.Hazard,
and
O.B.Peersen
(1994).
Molecular tuning of ion binding to calcium signaling proteins.
|
| |
Q Rev Biophys,
27,
219-290.
|
|
|
|
|
|
|
N.J.Skelton,
J.Kördel,
M.Akke,
S.Forsén,
and
W.J.Chazin
(1994).
Signal transduction versus buffering activity in Ca(2+)-binding proteins.
|
| |
Nat Struct Biol,
1,
239-245.
|
|
|
|
|
|
|
S.M.Gagné,
S.Tsuda,
M.X.Li,
M.Chandra,
L.B.Smillie,
and
B.D.Sykes
(1994).
Quantification of the calcium-induced secondary structural changes in the regulatory domain of troponin-C.
|
| |
Protein Sci,
3,
1961-1974.
|
|
|
|
|
|
|
J.A.Tainer,
V.A.Roberts,
and
E.D.Getzoff
(1992).
Protein metal-binding sites.
|
| |
Curr Opin Biotechnol,
3,
378-387.
|
|
|
|
|
|
|
W.J.Chazin
(1992).
NMR structures and methodology.
|
| |
Curr Opin Biotechnol,
3,
326-332.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
|
Links
