S100 Family: 2.40.30.10.5.1.1.1

Representative domain: 1f20A03

Classification Lineage (2.40.30.10.5.1.1.1)

CATH Code	Level Description	Links
2	Mainly Beta
2.40	Beta Barrel
2.40.30	Elongation Factor Tu (Ef-tu); domain 3
2.40.30.10	Translation factors	Gene3D
2.40.30.10.5
2.40.30.10.5.1
2.40.30.10.5.1.1
2.40.30.10.5.1.1.1

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 2.40.30.10.5.1.1.1 (3)

CATH code	Domain ID	Keywords
2.40.30.10.5.1.1.1.1	1f20A03	response to vitamin E, mitochondrial outer membrane, positive regulation of vasodilation, cytosol, response to organic nitrogen, regulation of sensory perception of pain, flavin adenine dinucleotide binding, response to ethanol, perinuclear region of cytoplasm, aging, response to hypoxia, synapse, negative regulation of blood pressure, Nitric-oxide synthase., response to estrogen stimulus, response to heat, Nitric oxide synthase, brain, Rattus norvegicus, sarcolemma, heme binding, arginine catabolic process, negative regulation of insulin secretion, nitric-oxide synthase activity, azurophil granule, nitric oxide biosynthetic process, FMN binding, protein homodimerization activity, calmodulin binding, enzyme binding, nuclear membrane, response to organic cyclic substance, negative regulation of heart contraction, photoreceptor inner segment, cadmium ion binding, amino acid binding, NADP or NADPH binding
2.40.30.10.5.1.1.1.2	1tllA03	mitochondrial outer membrane, response to vitamin E, cytosol, positive regulation of vasodilation, response to organic nitrogen, flavin adenine dinucleotide binding, regulation of sensory perception of pain, response to ethanol, perinuclear region of cytoplasm, response to hypoxia, aging, synapse, negative regulation of blood pressure, response to heat, response to estrogen stimulus, Nitric-oxide synthase., Nitric oxide synthase, brain, Rattus norvegicus, sarcolemma, heme binding, arginine catabolic process, negative regulation of insulin secretion, nitric-oxide synthase activity, azurophil granule, FMN binding, nitric oxide biosynthetic process, calmodulin binding, protein homodimerization activity, response to organic cyclic substance, nuclear membrane, enzyme binding, negative regulation of heart contraction, photoreceptor inner segment, amino acid binding, NADP or NADPH binding, cadmium ion binding
2.40.30.10.5.1.1.1.3	1tllB03	nitric-oxide synthase activity, negative regulation of insulin secretion, arginine catabolic process, azurophil granule, negative regulation of heart contraction, enzyme binding, nuclear membrane, response to organic cyclic substance, protein homodimerization activity, calmodulin binding, nitric oxide biosynthetic process, FMN binding, cadmium ion binding, NADP or NADPH binding, amino acid binding, photoreceptor inner segment, response to ethanol, regulation of sensory perception of pain, flavin adenine dinucleotide binding, response to organic nitrogen, cytosol, positive regulation of vasodilation, response to vitamin E, mitochondrial outer membrane, aging, response to hypoxia, perinuclear region of cytoplasm, Nitric-oxide synthase., response to heat, response to estrogen stimulus, negative regulation of blood pressure, synapse, heme binding, Rattus norvegicus, sarcolemma, Nitric oxide synthase, brain

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=2.40.30.10.5.1.1.1

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: 2.40.30.10.5.1.1.1

Classification Lineage (2.40.30.10.5.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 2.40.30.10.5.1.1.1 (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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