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PDBsum entry 2cnp
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Calcium-binding protein
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PDB id
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2cnp
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Contents |
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* Residue conservation analysis
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PDB id:
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Calcium-binding protein
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Title:
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High resolution solution structure of apo rabbit calcyclin, nmr, 22 structures
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Structure:
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Calcyclin. Chain: a, b. Synonym: 2a9, cacy, s100a6, pra. Engineered: yes
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Source:
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Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Organ: lung. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
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NMR struc:
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22 models
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Authors:
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L.Maler,B.C.M.Potts,W.J.Chazin
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Key ref:
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L.Mäler
et al.
(1999).
High resolution solution structure of apo calcyclin and structural variations in the S100 family of calcium-binding proteins.
J Biomol Nmr,
13,
233-247.
PubMed id:
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Date:
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07-Jan-99
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Release date:
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22-Jul-99
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PROCHECK
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Headers
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References
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P30801
(S10A6_RABIT) -
Protein S100-A6 from Oryctolagus cuniculus
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Seq:
Struc:
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90 a.a.
90 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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J Biomol Nmr
13:233-247
(1999)
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PubMed id:
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High resolution solution structure of apo calcyclin and structural variations in the S100 family of calcium-binding proteins.
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L.Mäler,
B.C.Potts,
W.J.Chazin.
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ABSTRACT
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The three-dimensional solution structure of apo rabbit lung calcyclin has been
refined to high resolution through the use of heteronuclear NMR spectroscopy and
13C, 15N-enriched protein. Upon completing the assignment of virtually all of
the 15N, 13C and 1H NMR resonances, the solution structure was determined from a
combination of 2814 NOE-derived distance constraints, and 272 torsion angle
constraints derived from scalar couplings. A large number of critical
inter-subunit NOEs (386) were identified from 13C-select, 13C-filtered NOESY
experiments, providing a highly accurate dimer interface. The combination of
distance geometry and restrained molecular dynamics calculations yielded
structures with excellent agreement with the experimental data and high
precision (rmsd from the mean for the backbone atoms in the eight helices: 0.33
A). Calcyclin exhibits a symmetric dimeric fold of two identical 90 amino acid
subunits, characteristic of the S100 subfamily of EF-hand Ca(2+)-binding
proteins. The structure reveals a readily identified pair of putative sites for
binding of Zn2+. In order to accurately determine the structural features that
differentiate the various S100 proteins, distance difference matrices and
contact maps were calculated for the NMR structural ensembles of apo calcyclin
and rat and bovine S100B. These data show that the most significant variations
among the structures are in the positioning of helix III and in loops, the
regions with least sequence similarity. Inter-helical angles and distance
differences for the proteins show that the positioning of helix III of calcyclin
is most similar to that of bovine S100B, but that the helix interfaces are more
closely packed in calcyclin than in either S100B structure. Surprisingly large
differences were found in the positioning of helix III in the two S100B
structures, despite there being only four non-identical residues, suggesting
that one or both of the S100B structures requires further refinement.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.B.Zimmer,
and
D.J.Weber
(2010).
The Calcium-Dependent Interaction of S100B with Its Protein Targets.
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Cardiovasc Psychiatry Neurol,
2010,
0.
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N.T.Wright,
B.R.Cannon,
D.B.Zimmer,
and
D.J.Weber
(2009).
S100A1: Structure, Function, and Therapeutic Potential.
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Curr Chem Biol,
3,
138-145.
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S.Malik,
M.Revington,
S.P.Smith,
and
G.S.Shaw
(2008).
Analysis of the structure of human apo-S100B at low temperature indicates a unimodal conformational distribution is adopted by calcium-free S100 proteins.
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Proteins,
73,
28-42.
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PDB code:
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V.N.Malashkevich,
K.M.Varney,
S.C.Garrett,
P.T.Wilder,
D.Knight,
T.H.Charpentier,
U.A.Ramagopal,
S.C.Almo,
D.J.Weber,
and
A.R.Bresnick
(2008).
Structure of Ca2+-bound S100A4 and its interaction with peptides derived from nonmuscle myosin-IIA.
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Biochemistry,
47,
5111-5126.
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PDB code:
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S.C.Garrett,
K.M.Varney,
D.J.Weber,
and
A.R.Bresnick
(2006).
S100A4, a mediator of metastasis.
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J Biol Chem,
281,
677-680.
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D.V.Venkitaramani,
D.B.Fulton,
A.H.Andreotti,
K.M.Johansen,
and
J.Johansen
(2005).
Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium-binding protein.
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Protein Sci,
14,
1894-1901.
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PDB codes:
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A.C.Dempsey,
M.P.Walsh,
and
G.S.Shaw
(2003).
Unmasking the annexin I interaction from the structure of Apo-S100A11.
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Structure,
11,
887-897.
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PDB code:
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D.B.Zimmer,
P.Wright Sadosky,
and
D.J.Weber
(2003).
Molecular mechanisms of S100-target protein interactions.
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Microsc Res Tech,
60,
552-559.
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J.C.Deloulme,
B.J.Gentil,
and
J.Baudier
(2003).
Monitoring of S100 homodimerization and heterodimeric interactions by the yeast two-hybrid system.
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Microsc Res Tech,
60,
560-568.
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M.D.Ohi,
C.W.Vander Kooi,
J.A.Rosenberg,
W.J.Chazin,
and
K.L.Gould
(2003).
Structural insights into the U-box, a domain associated with multi-ubiquitination.
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Nat Struct Biol,
10,
250-255.
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PDB code:
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C.Sopalla,
N.Leukert,
C.Sorg,
and
C.Kerkhoff
(2002).
Evidence for the involvement of the unique C-tail of S100A9 in the binding of arachidonic acid to the heterocomplex S100A8/A9.
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Biol Chem,
383,
1895-1905.
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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.
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J Biol Chem,
277,
33092-33098.
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L.R.Otterbein,
J.Kordowska,
C.Witte-Hoffmann,
C.L.Wang,
and
R.Dominguez
(2002).
Crystal structures of S100A6 in the Ca(2+)-free and Ca(2+)-bound states: the calcium sensor mechanism of S100 proteins revealed at atomic resolution.
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Structure,
10,
557-567.
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PDB codes:
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S.Yui,
Y.Nakatani,
M.J.Hunter,
W.J.Chazin,
and
M.Yamazaki
(2002).
Implication of extracellular zinc exclusion by recombinant human calprotectin (MRP8 and MRP14) from target cells in its apoptosis-inducing activity.
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Mediators Inflamm,
11,
165-172.
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K.G.Inman,
D.M.Baldisseri,
K.E.Miller,
and
D.J.Weber
(2001).
Backbone dynamics of the calcium-signaling protein apo-S100B as determined by 15N NMR relaxation.
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Biochemistry,
40,
3439-3448.
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O.V.Moroz,
A.A.Antson,
G.N.Murshudov,
N.J.Maitland,
G.G.Dodson,
K.S.Wilson,
I.Skibshøj,
E.M.Lukanidin,
and
I.B.Bronstein
(2001).
The three-dimensional structure of human S100A12.
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Acta Crystallogr D Biol Crystallogr,
57,
20-29.
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PDB code:
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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.
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Proteins,
37,
499-507.
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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.
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Links
