S100 Family: 1.20.1250.10.10.1.1.1

Representative domain: 1aluA00

Classification Lineage (1.20.1250.10.10.1.1.1)

CATH Code	Level Description	Links
1	Mainly Alpha
1.20	Up-down Bundle
1.20.1250	Growth Hormone; Chain: A;
1.20.1250.10		Gene3D
1.20.1250.10.10
1.20.1250.10.10.1
1.20.1250.10.10.1.1
1.20.1250.10.10.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	4

Non-Redundant Representatives (4)
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 1.20.1250.10.10.1.1.1 (4)

CATH code	Domain ID	Keywords
1.20.1250.10.10.1.1.1.1	1aluA00	hepatic immune response, regulation of vascular endothelial growth factor production, Graft-versus-host disease, positive regulation of interleukin-6 production, cytokine activity, Chagas disease, neutrophil apoptosis, NOD-like receptor signaling pathway, response to glucocorticoid stimulus, positive regulation of translation, interleukin-6 receptor complex, Jak-STAT signaling pathway, positive regulation of transcription factor activity, positive regulation of peptidyl-serine phosphorylation, positive regulation of tyrosine phosphorylation of Stat3 protein, positive regulation of anti-apoptosis, defense response to virus, positive regulation of chemokine production, neuron projection development, Toll-like receptor signaling pathway, Prion diseases, positive regulation of B cell activation, negative regulation of cell proliferation, Intestinal immune network for IgA production, acute-phase response, Cytokine-cytokine receptor interaction, defense response to Gram-positive bacterium, positive regulation of T cell proliferation, positive regulation of transcription from RNA polymerase II promoter, interleukin-6-mediated signaling pathway, positive regulation of osteoblast differentiation, negative regulation of collagen biosynthetic process, Pathways in cancer, negative regulation of apoptosis, interleukin 6, positive regulation of gene-specific transcription, Homo sapiens, Interleukin-6, positive regulation of MAPKKK cascade, Cytosolic DNA-sensing pathway, Hematopoietic cell lineage, Hypertrophic cardiomyopathy (HCM), positive regulation of smooth muscle cell proliferation, positive regulation of immunoglobulin secretion, positive regulation of acute inflammatory response, growth factor activity, platelet activation, defense response to Gram-negative bacterium, extracellular space, response to peptidoglycan
1.20.1250.10.10.1.1.1.2	1p9mB00	interleukin 6, Pathways in cancer, negative regulation of apoptosis, positive regulation of osteoblast differentiation, negative regulation of collagen biosynthetic process, positive regulation of transcription from RNA polymerase II promoter, interleukin-6-mediated signaling pathway, defense response to Gram-negative bacterium, response to peptidoglycan, extracellular space, positive regulation of immunoglobulin secretion, positive regulation of acute inflammatory response, growth factor activity, platelet activation, Cytosolic DNA-sensing pathway, Hematopoietic cell lineage, Hypertrophic cardiomyopathy (HCM), positive regulation of smooth muscle cell proliferation, positive regulation of gene-specific transcription, Homo sapiens, Interleukin-6, positive regulation of MAPKKK cascade, Jak-STAT signaling pathway, positive regulation of peptidyl-serine phosphorylation, positive regulation of transcription factor activity, positive regulation of tyrosine phosphorylation of Stat3 protein, NOD-like receptor signaling pathway, positive regulation of translation, response to glucocorticoid stimulus, interleukin-6 receptor complex, cytokine activity, Chagas disease, neutrophil apoptosis, hepatic immune response, regulation of vascular endothelial growth factor production, Graft-versus-host disease, positive regulation of interleukin-6 production, acute-phase response, Cytokine-cytokine receptor interaction, defense response to Gram-positive bacterium, positive regulation of T cell proliferation, Intestinal immune network for IgA production, Toll-like receptor signaling pathway, Prion diseases, positive regulation of B cell activation, negative regulation of cell proliferation, positive regulation of anti-apoptosis, defense response to virus, positive regulation of chemokine production, neuron projection development
1.20.1250.10.10.1.1.1.3	1il6A00	Pathways in cancer, negative regulation of apoptosis, interleukin 6, positive regulation of transcription from RNA polymerase II promoter, interleukin-6-mediated signaling pathway, positive regulation of osteoblast differentiation, negative regulation of collagen biosynthetic process, positive regulation of immunoglobulin secretion, positive regulation of acute inflammatory response, growth factor activity, platelet activation, defense response to Gram-negative bacterium, response to peptidoglycan, extracellular space, positive regulation of gene-specific transcription, Homo sapiens, Interleukin-6, positive regulation of MAPKKK cascade, Cytosolic DNA-sensing pathway, Hematopoietic cell lineage, Hypertrophic cardiomyopathy (HCM), positive regulation of smooth muscle cell proliferation, NOD-like receptor signaling pathway, positive regulation of translation, response to glucocorticoid stimulus, interleukin-6 receptor complex, Jak-STAT signaling pathway, positive regulation of transcription factor activity, positive regulation of peptidyl-serine phosphorylation, positive regulation of tyrosine phosphorylation of Stat3 protein, hepatic immune response, regulation of vascular endothelial growth factor production, Graft-versus-host disease, positive regulation of interleukin-6 production, cytokine activity, Chagas disease, neutrophil apoptosis, Intestinal immune network for IgA production, acute-phase response, Cytokine-cytokine receptor interaction, defense response to Gram-positive bacterium, positive regulation of T cell proliferation, positive regulation of anti-apoptosis, defense response to virus, positive regulation of chemokine production, neuron projection development, Toll-like receptor signaling pathway, Prion diseases, positive regulation of B cell activation, negative regulation of cell proliferation
1.20.1250.10.10.1.1.1.4	2il6A00	Chagas disease, neutrophil apoptosis, cytokine activity, positive regulation of interleukin-6 production, Graft-versus-host disease, regulation of vascular endothelial growth factor production, hepatic immune response, positive regulation of tyrosine phosphorylation of Stat3 protein, Jak-STAT signaling pathway, positive regulation of transcription factor activity, positive regulation of peptidyl-serine phosphorylation, interleukin-6 receptor complex, NOD-like receptor signaling pathway, positive regulation of translation, response to glucocorticoid stimulus, negative regulation of cell proliferation, Prion diseases, positive regulation of B cell activation, Toll-like receptor signaling pathway, neuron projection development, positive regulation of chemokine production, defense response to virus, positive regulation of anti-apoptosis, positive regulation of T cell proliferation, Cytokine-cytokine receptor interaction, defense response to Gram-positive bacterium, acute-phase response, Intestinal immune network for IgA production, negative regulation of collagen biosynthetic process, positive regulation of osteoblast differentiation, interleukin-6-mediated signaling pathway, positive regulation of transcription from RNA polymerase II promoter, interleukin 6, Pathways in cancer, negative regulation of apoptosis, Hypertrophic cardiomyopathy (HCM), positive regulation of smooth muscle cell proliferation, Hematopoietic cell lineage, Cytosolic DNA-sensing pathway, Homo sapiens, Interleukin-6, positive regulation of MAPKKK cascade, positive regulation of gene-specific transcription, response to peptidoglycan, extracellular space, defense response to Gram-negative bacterium, platelet activation, growth factor activity, positive regulation of acute inflammatory response, positive regulation of immunoglobulin secretion

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=1.20.1250.10.10.1.1.1

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: 1.20.1250.10.10.1.1.1

Classification Lineage (1.20.1250.10.10.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 1.20.1250.10.10.1.1.1 (4)

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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