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Types of Information That Are Stored in the Relational Database That Supports the EF-Hand Calcium-Binding Proteins Data Library

All of these types of information can be submitted to the data library via the online form-based system, except interhelical angles and inter-residue distances.

Information Type
(Linked to Example on Pages)
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Descriptive Information
Additional Name
alternative name for the protein
(for S100A9)
abbreviation for any name for the protein
CaM (for calmodulin)
Chemical and Physical Information
calculated or measured isoelectric point for the protein
4.7 (for hippocalcin)
Number of Functional Calcium-Binding Sites
number of binding loops that are able to bind calcium; "0" is an acceptable input
4 (for caltractin)
Metal Binding Constants
macroscopic binding constants for any metal; must input solution conditions
K1 = 5.00 x 104; K2 = 1.58 x 106; K3 = 1.00 x 104; K4 = 2.00 x 105 (for calmodulin, at high salt)
K1 = 9.50 x 104; K2 = 9.50 x 104 (for parvalbumin, at medium salt)
Protein Stability
the free energy of unfolding, and the cooperativity of the unfolding transition (if available)
free energy of unfolding: 4.78 +/- 0.24 kcal/mol, cooperativity of unfolding: 0.908 kcal/(mol M) (for calbindin D9k)
Post-Translational Modification
any change from the simple protein sequence that occurs after translation
phosphorylation on Thr113 (for S100A9)
Biological Information
Source Organism
species in which protein is found
Schistosoma japonicum, Homo sapiens, and Cricetulus longicaudatuas (for sorcin)
No (but inclusion of SWISS-PROT entry code is encouraged)
Source Tissue
tissue in which protein is found
brain (for calbindin D28k, in mammals)
Subcellular Localization
tissue in which protein is found
basal bodies (microtubule organizing center) (for caltractin, in Chlamydomonas reinhardtii
Regulation of Activity or Expression
molecule that regulates the protein, either by modulating its activty or its expression
Vitamin D (upregulates expression) (for calbindin D9k, in all sources)
Genomic Information
Gene Length
length of entire gene (not just the cDNA), in kilobases
13 kb (for hippocalcin from rat, GenBank code D12573)
Gene Structure
number, positioning, and length of introns
intron 1 is in the 5'-untranslated region, intron 2 precedes residue 13, intron 3 precedes residue 64 (for S100A5 from human, GenBank codes Z18950, Z18949)
element in the gene that regulates expression of the gene
CCAAT-like element, 72 bp upstream from transcription start site (putative) (for calbindin D9k, in rat, GenBank code X16635)
Gene Copies
number of expressed copies of a gene
3 gene copies (code for an indentical protein) (for human calmodulin)
naturally occuring allele of a gene, expressed as a mutation in the protein sequence
D72E (for S100A5)
Chromosomal Localization
chromosome on which gene is found, and localization on the chromosome if available
sub-band E region of chromosome 15 (for alpha lineage parvalbumin from mouse, GenBank code X54613)
Functional Information
General Note on Function
comments about function that do not fit into the other categories,; comparisons of functional properties of various proteins
The calmodulin-like domain is covalently attached to its "target" kinase (for CDPK)
Biological Role of Protein
role of protein in a biological process
remodeling and disassembling the cytoskeleton (for calpain)
Signal Transduction Pathway in Which Protein is Involved
involvement of protein in a signal transduction pathway; molecule with which protein interacts in this pathway should be included if available
inflammation signal transduction pathway: interacts with arachidonic acid (for S100A8)
Disease State in Which Protein is Involved
involvement of protein in a disease state; assumed to refer to humans
psoriasis (for S100A7)
Target Molecule of Protein
molecule with which protein interacts in a biologically meaningful manner; can include drugs
phosphoglucomutase (for S100A1)
Target Activation by Wildtype Protein
ability of protein to activate a particular target, and K(act) and V(max) if available
calmodulin activates calcium/calmodulin-dependent protein kinase II
Structural Information
Calcium Coordination by Protein
coordination type and calcium ligands for each EF-hand in the protein
calcium coordination in calmodulin
No (but PDB file must already be stored in database)
Nature of a Conformational Change
conformational change observed in comparing two states of a protein (such as apo and calcium-loaded)
calcium-induced conformational change in calmodulin
Hydrogen Bonds Observed
hydrogen bonds observed in a given structure of a protein
hydrogen bonds in various calbindin D9k structures no online submission
Interhelical Angles
Angles between the four helices in a two EF-hand structural unit.
interhelical angles in various calbindin D9k structures
no online submission
Inter-residue Distances
Distance between the centers of geometry of two residues in a structure
inter-residue distances in the 1CLL structure of calcium-loaded calmodulin
no online submission
Mutant Information
Existence of a Mutant
report existence a mutant to the database
various mutations of CaBPs Yes
Phenotypic Effect of Mutant
basic effect of a mutant
F92A + F140A (mutant of calmodulin)
Target Activation by Mutant
ability of a mutant to activate a given target; includes per cent activation (relative to wildtype), K(act), and V(max), when available
M36L (mutant of calmodulin)
Please note: all of the other types of information that can pertain to a mutant can be submitted to the database as for any other protein

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