S100 Family: 2.30.30.40.5.1.1.1

Representative domain: 1y0mA00

Classification Lineage (2.30.30.40.5.1.1.1)

CATH Code	Level Description	Links
2	Mainly Beta
2.30	Roll
2.30.30	SH3 type barrels.
2.30.30.40	SH3 Domains	Gene3D
2.30.30.40.5
2.30.30.40.5.1
2.30.30.40.5.1.1
2.30.30.40.5.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	3

Non-Redundant Representatives (3)
Functional Families
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What is a Non-Redundant Representative?

CATH is a tree-like organisation of nodes that begins with the class node (i.e. the first branch-point of the tree) and ends with the domain nodes (i.e. the leaves of the tree). Each node below the class have a parent that they belong to, e.g. the parent of the H level (Homologous superfamily) is the T (Topology). Additionally, each node above the domains have child nodes that belong to them, e.g. the child nodes of a given H (Homologous superfamily) level are the S35 families (domains clustered at > 35% sequence identity).

S100 Count Entries in S100 Family 2.30.30.40.5.1.1.1 (3)

CATH code	Domain ID	Keywords
2.30.30.40.5.1.1.1.1	1y0mA00	calcium ion transport, Neurotrophin signaling pathway, Leukocyte transendothelial migration, positive regulation of epithelial cell migration, response to morphine, phospholipase C, gamma [EC:3.1.4.11], T cell receptor signaling pathway, Inositol phosphate metabolism, Glioma, Pathways in cancer, positive regulation of calcium ion transport via store-operated calcium channel activity, ErbB signaling pathway, response to hydrogen peroxide, Metabolic pathways, inositol trisphosphate biosynthetic process, Calcium signaling pathway, 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-1, response to gravity, vesicle-mediated transport, Fc gamma R-mediated phagocytosis, VEGF signaling pathway, phosphoprotein binding, response to organic nitrogen, Natural killer cell mediated cytotoxicity, insulin receptor binding, Phosphoinositide phospholipase C., Non-small cell lung cancer, Phosphatidylinositol signaling system, Rattus norvegicus, cytoplasm, Fc epsilon RI signaling pathway
2.30.30.40.5.1.1.1.2	1ywpA00	phospholipase C, gamma [EC:3.1.4.11], T cell receptor signaling pathway, calcium ion transport, Leukocyte transendothelial migration, Neurotrophin signaling pathway, response to morphine, positive regulation of epithelial cell migration, Metabolic pathways, inositol trisphosphate biosynthetic process, Inositol phosphate metabolism, ErbB signaling pathway, response to hydrogen peroxide, Glioma, Pathways in cancer, positive regulation of calcium ion transport via store-operated calcium channel activity, phosphoprotein binding, VEGF signaling pathway, response to organic nitrogen, Calcium signaling pathway, 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-1, response to gravity, Fc gamma R-mediated phagocytosis, vesicle-mediated transport, cytoplasm, Fc epsilon RI signaling pathway, Natural killer cell mediated cytotoxicity, Phosphoinositide phospholipase C., insulin receptor binding, Phosphatidylinositol signaling system, Rattus norvegicus, Non-small cell lung cancer
2.30.30.40.5.1.1.1.3	1ywoA00	Fc epsilon RI signaling pathway, cytoplasm, insulin receptor binding, Phosphoinositide phospholipase C., Non-small cell lung cancer, Phosphatidylinositol signaling system, Rattus norvegicus, Natural killer cell mediated cytotoxicity, response to organic nitrogen, VEGF signaling pathway, phosphoprotein binding, vesicle-mediated transport, Fc gamma R-mediated phagocytosis, Calcium signaling pathway, 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-1, response to gravity, Metabolic pathways, inositol trisphosphate biosynthetic process, Glioma, Pathways in cancer, positive regulation of calcium ion transport via store-operated calcium channel activity, ErbB signaling pathway, response to hydrogen peroxide, Inositol phosphate metabolism, phospholipase C, gamma [EC:3.1.4.11], T cell receptor signaling pathway, Neurotrophin signaling pathway, Leukocyte transendothelial migration, positive regulation of epithelial cell migration, response to morphine, calcium ion transport

The information on Functional Families (FunFams) is currently being updated and will be released by the end of March 2012. The pages will include the following features:

Multiple alignments for each functional family
Representative structure for each functional with known catalytic and interface residues highlighted, along with conserved residues predicted by scorecons
Detailed functional information on diversity and conservation within Functional families
Multi-domain architectures

In the meantime, please find a summary of information on the FunFams and protein networks within this superfamily on the Gene3D pages:

http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=2.30.30.40.5.1.1.1

What is a Non-Redundant Representative?

Why can't I have a multiple structural alignment of the whole superfamily?

The simple answer is that some of the larger superfamilies in CATH comprise relatives which are very structurally diverse, having different secondary structure embellishments. Attempting to provide a global alignment of all domains in the superfamily would result in poor quality alignments. As a result, structural alignments in CATH are generated by first clustering together the structures that have at least some recognisable structural similarity using a normalised RMSD score (SIMAX = RMSDxNumber of residues in the largest domain/number of aligned residues) less than a given cutoff.

What is an Close Structural Cluster?

A Close Structural Cluster describes a cluster of two or more CATH domains that have been grouped together due to their close structural similarity (SIMAX score < 5Å where SIMAX = RMSD x Number of residues in the larger domain/number of aligned residues).

What is a Distant Structural Cluster?

A Distant Structural Cluster describes a cluster of two or CATH domains that have been grouped together with a more relaxed structural similarity threshold to investigate more distant evolutionary similarities (SIMAX score < 5Å where SIMAX = RMSD x Number of residues in the larger domain/number of aligned residues).

What is a Structural Neighbour?

The term "structural neighbour" is used here to describe two CATH domains that share a degree of structural similarity. The SSAP algorithm is used to calculate this similarity and works by generating a structure-based pairwise alignment of the two domains then scoring this alignment using a RMSD score which has been normalised by the length of the larger domain divided by the number of aligned residues (SIMAX).

S100 Family: 2.30.30.40.5.1.1.1

Classification Lineage (2.30.30.40.5.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 2.30.30.40.5.1.1.1 (3)

What is a Non-Redundant Representative?

Why can't I have a multiple structural alignment of the whole superfamily?

What is an Close Structural Cluster?

What is a Distant Structural Cluster?

What is a Structural Neighbour?

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