 |
PDBsum entry 2bca
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Calcium-binding protein
|
PDB id
|
|
|
|
2bca
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
J Mol Biol
231:711-734
(1993)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
High-resolution structure of calcium-loaded calbindin D9k.
|
|
J.Kördel,
N.J.Skelton,
M.Akke,
W.J.Chazin.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The three-dimensional solution structure of calcium-loaded calbindin D9k has
been determined using experimental constraints obtained from nuclear magnetic
resonance spectroscopy. A total of 1176 constraints (16 per residue overall, 32
per residue for the core residues) was used for the final refinement, including
1002 distance and 174 dihedral angle constraints. In addition, 23 hydrogen bond
constraints were used for the generation of initial structures. Stereospecific
assignments were made for 37 of 61 (61%) prochiral methylene protons and the
methyl groups of all three valine residues and five out of 12 leucine residues.
These constraints were used as input for a series of calculations of
three-dimensional structures using a combination of distance geometry and
restrained molecular dynamics. The 33 best structures selected for further
analysis have no distance constraint violations greater than 0.3 A and good
local geometries as reflected by low total energies (< or = -1014 kcal/mol in
the AMBER 4.0 force field). The core of the protein consists of four
well-defined helices with root-mean-square deviations from the average of 0.45 A
for the N, C alpha and C' backbone atoms. These helices are packed in an
antiparallel fashion to form two helix-loop-helix calcium-binding motifs, termed
EF-hands. The two EF-hands are joined at one end by a ten-residue linker
segment, and at the other by a short beta-type interaction between the two
calcium-binding loops. Overall, the average solution structure of calbindin D9k
is very similar to the crystal structure, with a pairwise root-mean-square
deviation of 0.85 A for the N, C alpha and C' backbone atoms of the four
helices. The differences that are observed between the solution and the crystal
structures are attributed to specific crystal contacts, increased side-chain
flexibility in solution, or artifacts arising from molecular dynamics refinement
of the solution structures in vacuo.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
N.A.Oktaviani,
R.Otten,
K.Dijkstra,
R.M.Scheek,
E.Thulin,
M.Akke,
and
F.A.Mulder
(2011).
100% complete assignment of non-labile (1)H, (13)C, and (15)N signals for calcium-loaded calbindin D (9k) P43G.
|
| |
Biomol NMR Assign,
5,
79-84.
|
|
|
|
|
|
|
E.Johnson,
L.Bruschweiler-Li,
S.A.Showalter,
G.W.Vuister,
F.Zhang,
and
R.Brüschweiler
(2008).
Structure and dynamics of Ca2+-binding domain 1 of the Na+/Ca2+ exchanger in the presence and in the absence of Ca2+.
|
| |
J Mol Biol,
377,
945-955.
|
|
|
|
|
|
|
G.D.Kutuzova,
S.Akhter,
S.Christakos,
J.Vanhooke,
C.Kimmel-Jehan,
and
H.F.Deluca
(2006).
Calbindin D(9k) knockout mice are indistinguishable from wild-type mice in phenotype and serum calcium level.
|
| |
Proc Natl Acad Sci U S A,
103,
12377-12381.
|
|
|
|
|
|
|
N.Powers,
and
J.H.Jensen
(2006).
Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.
|
| |
J Biomol NMR,
35,
39-51.
|
|
|
|
|
|
|
S.Balayssac,
B.Jiménez,
and
M.Piccioli
(2006).
Assignment strategy for fast relaxing signals: complete aminoacid identification in thulium substituted calbindin D 9K.
|
| |
J Biomol NMR,
34,
63-73.
|
|
|
|
|
|
|
D.Abergel,
and
G.Bodenhausen
(2005).
Predicting internal protein dynamics from structures using coupled networks of hindered rotators.
|
| |
J Chem Phys,
123,
204901.
|
|
|
|
|
|
|
G.Goch,
S.Vdovenko,
H.Kozłowska,
and
A.Bierzyñski
(2005).
Affinity of S100A1 protein for calcium increases dramatically upon glutathionylation.
|
| |
FEBS J,
272,
2557-2565.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
B.Jiménez,
L.Poggi,
and
M.Piccioli
(2003).
Monitoring the early steps of unfolding of dicalcium and mono-Ce3+-substituted forms of P43M calbindin D9k.
|
| |
Biochemistry,
42,
13066-13073.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.J.Price,
and
C.L.Brooks
(2002).
Modern protein force fields behave comparably in molecular dynamics simulations.
|
| |
J Comput Chem,
23,
1045-1057.
|
|
|
|
|
|
|
G.Fritz,
P.R.Mittl,
M.Vasak,
M.G.Grutter,
and
C.W.Heizmann
(2002).
The crystal structure of metal-free human EF-hand protein S100A3 at 1.7-A resolution.
|
| |
J Biol Chem,
277,
33092-33098.
|
|
|
|
|
|
|
L.S.Mizoue,
and
W.J.Chazin
(2002).
Engineering and design of ligand-induced conformational change in proteins.
|
| |
Curr Opin Struct Biol,
12,
459-463.
|
|
|
|
|
|
|
M.R.Nelson,
E.Thulin,
P.A.Fagan,
S.Forsén,
and
W.J.Chazin
(2002).
The EF-hand domain: a globally cooperative structural unit.
|
| |
Protein Sci,
11,
198-205.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Ababou,
and
J.R.Desjarlais
(2001).
Solvation energetics and conformational change in EF-hand proteins.
|
| |
Protein Sci,
10,
301-312.
|
|
|
|
|
|
|
I.Bertini,
Y.M.Lee,
C.Luchinat,
M.Piccioli,
and
L.Poggi
(2001).
Locating the metal ion in calcium-binding proteins by using cerium(III) as a probe.
|
| |
Chembiochem,
2,
550-558.
|
|
|
|
|
|
|
T.Kesvatera,
B.Jönsson,
E.Thulin,
and
S.Linse
(2001).
Focusing of the electrostatic potential at EF-hands of calbindin D(9k): titration of acidic residues.
|
| |
Proteins,
45,
129-135.
|
|
|
|
|
|
|
F.Fant,
W.F.Vranken,
and
F.A.Borremans
(1999).
The three-dimensional solution structure of Aesculus hippocastanum antimicrobial protein 1 determined by 1H nuclear magnetic resonance.
|
| |
Proteins,
37,
388-403.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.L.Yap,
J.B.Ames,
M.B.Swindells,
and
M.Ikura
(1999).
Diversity of conformational states and changes within the EF-hand protein superfamily.
|
| |
Proteins,
37,
499-507.
|
|
|
|
|
|
|
W.Klaus,
S.Grzesiek,
A.M.Labhardt,
P.Buchwald,
W.Hunziker,
M.D.Gross,
and
D.A.Kallick
(1999).
NMR investigation and secondary structure of domains I and II of rat brain calbindin D28k (1-93).
|
| |
Eur J Biochem,
262,
933-938.
|
|
|
|
|
|
|
B.B.Kragelund,
M.Jönsson,
G.Bifulco,
W.J.Chazin,
H.Nilsson,
B.E.Finn,
and
S.Linse
(1998).
Hydrophobic core substitutions in calbindin D9k: effects on Ca2+ binding and dissociation.
|
| |
Biochemistry,
37,
8926-8937.
|
|
|
|
|
|
|
D.S.Sem,
B.L.Baker,
E.J.Victoria,
D.S.Jones,
D.Marquis,
L.Yu,
J.Parks,
and
S.M.Coutts
(1998).
Structural characterization and optimization of antibody-selected phage library mimotopes of an antigen associated with autoimmune recurrent thrombosis.
|
| |
Biochemistry,
37,
16069-16081.
|
|
|
|
|
|
|
H.Matsumura,
T.Shiba,
T.Inoue,
S.Harada,
and
Y.Kai
(1998).
A novel mode of target recognition suggested by the 2.0 A structure of holo S100B from bovine brain.
|
| |
Structure,
6,
233-241.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Evenäs,
A.Malmendal,
E.Thulin,
G.Carlström,
and
S.Forsén
(1998).
Ca2+ binding and conformational changes in a calmodulin domain.
|
| |
Biochemistry,
37,
13744-13754.
|
|
|
|
|
|
|
M.R.Nelson,
and
W.J.Chazin
(1998).
An interaction-based analysis of calcium-induced conformational changes in Ca2+ sensor proteins.
|
| |
Protein Sci,
7,
270-282.
|
|
|
|
|
|
|
M.Sastry,
R.R.Ketchem,
O.Crescenzi,
C.Weber,
M.J.Lubienski,
H.Hidaka,
and
W.J.Chazin
(1998).
The three-dimensional structure of Ca(2+)-bound calcyclin: implications for Ca(2+)-signal transduction by S100 proteins.
|
| |
Structure,
6,
223-231.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.P.Smith,
and
G.S.Shaw
(1998).
A novel calcium-sensitive switch revealed by the structure of human S100B in the calcium-bound form.
|
| |
Structure,
6,
211-222.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Evenäs,
E.Thulin,
A.Malmendal,
S.Forsén,
and
G.Carlström
(1997).
NMR studies of the E140Q mutant of the carboxy-terminal domain of calmodulin reveal global conformational exchange in the Ca2+-saturated state.
|
| |
Biochemistry,
36,
3448-3457.
|
|
|
|
|
|
|
J.R.Martin,
F.A.Mulder,
Y.Karimi-Nejad,
J.van der Zwan,
M.Mariani,
D.Schipper,
and
R.Boelens
(1997).
The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site.
|
| |
Structure,
5,
521-532.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.Andersson,
A.Malmendal,
S.Linse,
I.Ivarsson,
S.Forsén,
and
L.A.Svensson
(1997).
Structural basis for the negative allostery between Ca(2+)- and Mg(2+)-binding in the intracellular Ca(2+)-receptor calbindin D9k.
|
| |
Protein Sci,
6,
1139-1147.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.Groves,
S.Linse,
E.Thulin,
and
S.Forsén
(1997).
A calbindin D9k mutant containing a novel structural extension: 1H nuclear magnetic resonance studies.
|
| |
Protein Sci,
6,
323-330.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
B.C.Potts,
J.Smith,
M.Akke,
T.J.Macke,
K.Okazaki,
H.Hidaka,
D.A.Case,
and
W.J.Chazin
(1995).
The structure of calcyclin reveals a novel homodimeric fold for S100 Ca(2+)-binding proteins.
|
| |
Nat Struct Biol,
2,
790-796.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Wimberly,
E.Thulin,
and
W.J.Chazin
(1995).
Characterization of the N-terminal half-saturated state of calbindin D9k: NMR studies of the N56A mutant.
|
| |
Protein Sci,
4,
1045-1055.
|
|
|
|
|
|
|
M.A.Eriksson,
T.Härd,
and
L.Nilsson
(1995).
On the pH dependence of amide proton exchange rates in proteins.
|
| |
Biophys J,
69,
329-339.
|
|
|
|
|
|
|
M.Zhang,
E.Thulin,
and
H.J.Vogel
(1994).
Reductive methylation and pKa determination of the lysine side chains in calbindin D9k.
|
| |
J Protein Chem,
13,
527-535.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
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
