PDBsum entry 3e3r

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protein metals Protein-protein interface(s) links
Calcium binding protein PDB id
Jmol PyMol
Protein chains
183 a.a. *
_CA ×9
Waters ×49
* Residue conservation analysis
PDB id:
Name: Calcium binding protein
Title: Crystal structure and biochemical characterization of recomb human calcyphosine delineates a novel ef-hand-containing pr family
Structure: Calcyphosin. Chain: a, b. Synonym: calcyphosine. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: caps. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.65Å     R-factor:   0.233     R-free:   0.277
Authors: H.Dong
Key ref:
H.Dong et al. (2008). Crystal-structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family. J Mol Biol, 383, 455-464. PubMed id: 18775726 DOI: 10.1016/j.jmb.2008.08.048
07-Aug-08     Release date:   26-Aug-08    
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Protein chains
Pfam   ArchSchema ?
Q13938  (CAYP1_HUMAN) -  Calcyphosin
189 a.a.
183 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     vesicle   3 terms 
  Biological process     intracellular signal transduction   1 term 
  Biochemical function     metal ion binding     2 terms  


DOI no: 10.1016/j.jmb.2008.08.048 J Mol Biol 383:455-464 (2008)
PubMed id: 18775726  
Crystal-structure and biochemical characterization of recombinant human calcyphosine delineates a novel EF-hand-containing protein family.
H.Dong, X.Li, Z.Lou, X.Xu, D.Su, X.Zhou, W.Zhou, M.Bartlam, Z.Rao.
Calcyphosine is an EF-hand protein involved in both Ca(2+)-phosphatidylinositol and cyclic AMP signal cascades, as well as in other cellular functions. The crystal structure of Ca(2+)-loaded calcyphosine was determined up to 2.65 A resolution and reveals a protein containing two pairs of Ca(2+)-binding EF-hand motifs. Calcyphosine shares a highly similar overall topology with calmodulin. However, there are striking differences between EF-hand 4, both N-terminal and C-terminal regions, and interdomain linkers. The C-terminal domain of calcyphosine possesses a large hydrophobic pocket in the presence of calcium ions that might be implicated in ligand binding, while its N-terminal hydrophobic pocket is almost shielded by an additional terminal helix. Calcyphosine is largely monomeric, regardless of the presence of Ca(2+). Differences in structure, oligomeric state in the presence and in the absence of Ca(2+), a highly conserved sequence with low similarity to other proteins, and phylogeny define a new EF-hand-containing family of calcyphosine proteins that extends from arthropods to humans.
  Selected figure(s)  
Figure 3.
Fig. 3. Comparison of calcyphosine with CaM. (a) Evolutionary relationship of calcyphosine with some of its nearest homologs. The sequences of some typical Ca^2 +-binding proteins with four EF-hand motifs were aligned using ClustalW, and the output tree file was displayed as a dendrogram using the program TreeView 1.6.6. The proteins are human proteins, unless stated in the dendrogram. (b) Superposition of calcyphosine and CaM (PDB code 1CLL) based on EF-hands 3 and 4. The color scheme is the same as for Fig. 1a, with CaM shown in magenta. All figures were prepared using PyMOL ( (c) Sequence alignment of calcyphosine with CaM. N-terminal additional α-helix αA and C-terminal inserted α-helix αJ are shown in blue boxes. Residues that correspond to the target recognition in the C-domain of CaM are highlighted with cyan spheres.
Figure 4.
Fig. 4. Superposition of calcyphosine with CaM–target complexes. (a) Superposition of the N-terminal and C-terminal domains of calcyphosine with the CaM–CaMKK complex. CaM is shown in magenta; the CaMKK α-helical fragment is shown in red; the calcyphosine N-terminal domain is shown in green; the C-terminal domain is shown in cyan. (b) Electrostatic surface representation of the CaM–EF complex and calcyphosine. The region of EF in contact with CaM is shown as a helical worm in the binding sites of CaM.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 383, 455-464) copyright 2008.  
  Figures were selected by an automated process.