PDBsum entry 1cb1

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protein links
Calcium-binding protein PDB id
Protein chain
78 a.a. *
* Residue conservation analysis
PDB id:
Name: Calcium-binding protein
Title: Three-dimensional solution structure of ca2+-loaded porcine calbindin d9k determined by nuclear magnetic resonance spectroscopy
Structure: Calbindin d9k. Chain: a. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823
NMR struc: 13 models
Authors: M.Akke,T.Drakenberg,W.J.Chazin
Key ref:
M.Akke et al. (1992). Three-dimensional solution structure of Ca(2+)-loaded porcine calbindin D9k determined by nuclear magnetic resonance spectroscopy. Biochemistry, 31, 1011-1020. PubMed id: 1734952 DOI: 10.1021/bi00119a009
13-Dec-91     Release date:   31-Oct-93    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P02632  (S100G_PIG) -  Protein S100-G
79 a.a.
78 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     vitamin D binding     3 terms  


DOI no: 10.1021/bi00119a009 Biochemistry 31:1011-1020 (1992)
PubMed id: 1734952  
Three-dimensional solution structure of Ca(2+)-loaded porcine calbindin D9k determined by nuclear magnetic resonance spectroscopy.
M.Akke, T.Drakenberg, W.J.Chazin.
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
16927295 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.  
12842051 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: 1nsh
10653637 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.  
10450090 L.Sandberg, and O.Edholm (1999).
A fast and simple method to calculate protonation states in proteins.
  Proteins, 36, 474-483.  
9562557 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: 1psr
9585577 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.  
9245399 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.  
  8931135 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.  
8652520 G.S.Shaw, and B.D.Sykes (1996).
NMR solution structure of a synthetic troponin C heterodimeric domain.
  Biochemistry, 35, 7429-7438.
PDB code: 1pon
8805590 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: 1cfp
8688416 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.  
7899550 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.  
7656053 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.  
  7703843 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.  
1368439 J.A.Tainer, V.A.Roberts, and E.D.Getzoff (1992).
Protein metal-binding sites.
  Curr Opin Biotechnol, 3, 378-387.  
1368432 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.