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 |
Description |
Example (Linked to Example on Pages) |
Reference Required? |
|---|---|---|---|
| Descriptive Information |
|||
| Additional Name |
alternative name for the protein |
(for S100A9) |
No |
| Abbreviation |
abbreviation for any name for the protein |
CaM (for calmodulin) |
No |
| Chemical and Physical Information |
|||
| pI |
calculated or measured isoelectric point for the protein |
4.7
(for hippocalcin) |
Yes |
| Number of Functional Calcium-Binding Sites |
number of binding loops that are able to bind calcium; "0" is
an acceptable input |
4
(for caltractin) |
Yes |
| 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) |
Yes |
| 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) |
Yes |
| Post-Translational Modification |
any change from the simple protein sequence that occurs after
translation |
phosphorylation on Thr113
(for S100A9) |
Yes |
| 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) |
Yes |
| Subcellular Localization |
tissue in which protein is found |
basal bodies (microtubule organizing center)
(for caltractin, in Chlamydomonas reinhardtii |
Yes |
| 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) |
Yes |
| Genomic Information |
|||
| Gene Length |
length of entire gene (not just the cDNA), in
kilobases |
13 kb (for hippocalcin from rat, GenBank code D12573) |
Yes |
| 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) |
Yes |
| Promoter |
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) |
Yes |
| Gene Copies |
number of expressed copies of a gene |
3 gene copies (code for an indentical protein)
(for human calmodulin) |
Yes |
| Allele |
naturally occuring allele of a gene, expressed as a mutation
in the protein sequence |
D72E (for S100A5) |
Yes |
| 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) |
Yes |
| 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) |
Yes |
| Biological Role of Protein |
role of protein in a biological process |
remodeling and disassembling the cytoskeleton
(for calpain) |
Yes |
| 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) |
Yes |
| Disease State in Which Protein is Involved |
involvement of protein in a disease state; assumed to refer
to humans |
psoriasis
(for S100A7) |
Yes |
| Target Molecule of Protein |
molecule with which protein interacts in a biologically
meaningful manner; can include drugs |
phosphoglucomutase
(for S100A1) |
Yes |
| 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 |
Yes |
| 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 |
Yes |
| 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) |
Yes |
| 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) |
Yes |
| 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 |
|||
 |
 |
 |
 |
 |
 |
 |
 |
 |
CaBP Data Library Home Page|
General Info|
Sequence Info|
Structural Info|
Analysis Tools|
Top of Current Section|
Search the Data Library|
Site Map|
Feedback