S100 Family: 3.90.520.10.1.1.1.1

Representative domain: 1ozjB00

Classification Lineage (3.90.520.10.1.1.1.1)

CATH Code	Level Description	Links
3	Alpha Beta
3.90	Alpha-Beta Complex
3.90.520	Smad3; Chain A
3.90.520.10	Smad3; Chain A	Gene3D
3.90.520.10.1
3.90.520.10.1.1
3.90.520.10.1.1.1
3.90.520.10.1.1.1.1

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 3.90.520.10.1.1.1.1 (4)

CATH code	Domain ID	Keywords
3.90.520.10.1.1.1.1.1	1ozjB00	TGF-beta signaling pathway, transforming growth factor beta receptor signaling pathway, sequence-specific DNA binding transcription factor activity, immune response, transport, Pancreatic cancer, positive regulation of transcription factor import into nucleus, negative regulation of mitotic cell cycle, Homo sapiens, Wnt signaling pathway, regulation of transforming growth factor beta receptor signaling pathway, transcription factor binding, evasion of host defenses by virus, cell cycle arrest, receptor complex, Endocytosis, protein kinase binding, Cell cycle, transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity, protein homodimerization activity, R-SMAD binding, wound healing, primary microRNA processing, Pathways in cancer, nuclear inner membrane, positive regulation of epithelial to mesenchymal transition, SMAD protein complex assembly, response to hypoxia, cell-cell junction organization, ubiquitin protein ligase binding, transforming growth factor beta receptor binding, promoter binding, Chagas disease, regulation of transforming growth factor-beta2 production, SMAD, mothers against DPP 2/3, induction of apoptosis, Adherens junction, co-SMAD binding, Mothers against decapentaplegic homolog 3, activation of caspase activity, negative regulation of cell growth, Colorectal cancer, Chronic myeloid leukemia
3.90.520.10.1.1.1.1.2	1ozjA00	Wnt signaling pathway, evasion of host defenses by virus, cell cycle arrest, transcription factor binding, regulation of transforming growth factor beta receptor signaling pathway, immune response, sequence-specific DNA binding transcription factor activity, TGF-beta signaling pathway, transforming growth factor beta receptor signaling pathway, Homo sapiens, Pancreatic cancer, positive regulation of transcription factor import into nucleus, negative regulation of mitotic cell cycle, transport, wound healing, primary microRNA processing, R-SMAD binding, nuclear inner membrane, Pathways in cancer, Cell cycle, transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity, Endocytosis, protein kinase binding, receptor complex, protein homodimerization activity, cell-cell junction organization, ubiquitin protein ligase binding, response to hypoxia, SMAD protein complex assembly, positive regulation of epithelial to mesenchymal transition, promoter binding, transforming growth factor beta receptor binding, Mothers against decapentaplegic homolog 3, Chronic myeloid leukemia, Colorectal cancer, negative regulation of cell growth, activation of caspase activity, SMAD, mothers against DPP 2/3, induction of apoptosis, Chagas disease, regulation of transforming growth factor-beta2 production, co-SMAD binding, Adherens junction
3.90.520.10.1.1.1.1.3	1mhdA00	Wnt signaling pathway, evasion of host defenses by virus, cell cycle arrest, transcription factor binding, regulation of transforming growth factor beta receptor signaling pathway, sequence-specific DNA binding transcription factor activity, TGF-beta signaling pathway, transforming growth factor beta receptor signaling pathway, immune response, transport, Homo sapiens, Pancreatic cancer, negative regulation of mitotic cell cycle, positive regulation of transcription factor import into nucleus, wound healing, primary microRNA processing, R-SMAD binding, Pathways in cancer, nuclear inner membrane, receptor complex, Cell cycle, transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity, Endocytosis, protein kinase binding, protein homodimerization activity, SMAD protein complex assembly, positive regulation of epithelial to mesenchymal transition, cell-cell junction organization, ubiquitin protein ligase binding, response to hypoxia, transforming growth factor beta receptor binding, promoter binding, Mothers against decapentaplegic homolog 3, negative regulation of cell growth, activation of caspase activity, Chronic myeloid leukemia, Colorectal cancer, Chagas disease, regulation of transforming growth factor-beta2 production, SMAD, mothers against DPP 2/3, induction of apoptosis, co-SMAD binding, Adherens junction
3.90.520.10.1.1.1.1.4	1mhdB00	Chronic myeloid leukemia, Colorectal cancer, negative regulation of cell growth, activation of caspase activity, Mothers against decapentaplegic homolog 3, co-SMAD binding, Adherens junction, SMAD, mothers against DPP 2/3, induction of apoptosis, Chagas disease, regulation of transforming growth factor-beta2 production, promoter binding, transforming growth factor beta receptor binding, cell-cell junction organization, ubiquitin protein ligase binding, response to hypoxia, SMAD protein complex assembly, positive regulation of epithelial to mesenchymal transition, nuclear inner membrane, Pathways in cancer, primary microRNA processing, wound healing, R-SMAD binding, protein homodimerization activity, Cell cycle, transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity, Endocytosis, protein kinase binding, receptor complex, cell cycle arrest, evasion of host defenses by virus, regulation of transforming growth factor beta receptor signaling pathway, transcription factor binding, Wnt signaling pathway, Homo sapiens, Pancreatic cancer, negative regulation of mitotic cell cycle, positive regulation of transcription factor import into nucleus, transport, immune response, sequence-specific DNA binding transcription factor activity, TGF-beta signaling pathway, transforming growth factor beta receptor signaling pathway

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=3.90.520.10.1.1.1.1

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: 3.90.520.10.1.1.1.1

Classification Lineage (3.90.520.10.1.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 3.90.520.10.1.1.1.1 (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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