S100 Family: 1.20.5.10.1.1.1.1

Representative domain: 1mz9A00

Classification Lineage (1.20.5.10.1.1.1.1)

CATH Code	Level Description	Links
1	Mainly Alpha
1.20	Up-down Bundle
1.20.5	Single alpha-helices involved in coiled-coils or other helix-helix interfaces
1.20.5.10		Gene3D
1.20.5.10.1
1.20.5.10.1.1
1.20.5.10.1.1.1
1.20.5.10.1.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	15

Non-Redundant Representatives (15)
Functional Families
Help

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 1.20.5.10.1.1.1.1 (15)

CATH code	Domain ID	Keywords
1.20.5.10.1.1.1.1.1	1mz9A00	Mus musculus, Cartilage oligomeric matrix protein
1.20.5.10.1.1.1.1.2	1mz9B00	Mus musculus, Cartilage oligomeric matrix protein
1.20.5.10.1.1.1.1.3	1mz9C00	Cartilage oligomeric matrix protein, Mus musculus
1.20.5.10.1.1.1.1.4	1mz9D00	Cartilage oligomeric matrix protein, Mus musculus
1.20.5.10.1.1.1.1.5	1mz9E00	Mus musculus, Cartilage oligomeric matrix protein
1.20.5.10.1.1.1.1.6	1vdfA00	Rattus norvegicus, extracellular matrix structural constituent, Focal adhesion, fibronectin binding, proteinaceous extracellular matrix, thrombospondin, ECM-receptor interaction, extracellular matrix organization, vitamin D binding, TGF-beta signaling pathway, Cartilage oligomeric matrix protein
1.20.5.10.1.1.1.1.7	1vdfB00	extracellular matrix organization, Cartilage oligomeric matrix protein, TGF-beta signaling pathway, vitamin D binding, Focal adhesion, extracellular matrix structural constituent, Rattus norvegicus, thrombospondin, ECM-receptor interaction, proteinaceous extracellular matrix, fibronectin binding
1.20.5.10.1.1.1.1.8	1vdfC00	Cartilage oligomeric matrix protein, TGF-beta signaling pathway, vitamin D binding, extracellular matrix organization, thrombospondin, ECM-receptor interaction, proteinaceous extracellular matrix, fibronectin binding, extracellular matrix structural constituent, Focal adhesion, Rattus norvegicus
1.20.5.10.1.1.1.1.9	1vdfD00	extracellular matrix organization, vitamin D binding, TGF-beta signaling pathway, Cartilage oligomeric matrix protein, Rattus norvegicus, extracellular matrix structural constituent, Focal adhesion, fibronectin binding, proteinaceous extracellular matrix, thrombospondin, ECM-receptor interaction
1.20.5.10.1.1.1.1.10	1vdfE00	extracellular matrix organization, vitamin D binding, TGF-beta signaling pathway, Cartilage oligomeric matrix protein, Rattus norvegicus, Focal adhesion, extracellular matrix structural constituent, fibronectin binding, proteinaceous extracellular matrix, ECM-receptor interaction, thrombospondin
1.20.5.10.1.1.1.1.11	1fbmA00	Rattus norvegicus, Focal adhesion, extracellular matrix structural constituent, proteinaceous extracellular matrix, fibronectin binding, ECM-receptor interaction, thrombospondin, extracellular matrix organization, vitamin D binding, Cartilage oligomeric matrix protein, TGF-beta signaling pathway
1.20.5.10.1.1.1.1.12	1fbmB00	thrombospondin, ECM-receptor interaction, fibronectin binding, proteinaceous extracellular matrix, extracellular matrix structural constituent, Focal adhesion, Rattus norvegicus, TGF-beta signaling pathway, Cartilage oligomeric matrix protein, vitamin D binding, extracellular matrix organization
1.20.5.10.1.1.1.1.13	1fbmC00	extracellular matrix organization, vitamin D binding, TGF-beta signaling pathway, Cartilage oligomeric matrix protein, Rattus norvegicus, extracellular matrix structural constituent, Focal adhesion, fibronectin binding, proteinaceous extracellular matrix, ECM-receptor interaction, thrombospondin
1.20.5.10.1.1.1.1.14	1fbmD00	Rattus norvegicus, Focal adhesion, extracellular matrix structural constituent, fibronectin binding, proteinaceous extracellular matrix, ECM-receptor interaction, thrombospondin, extracellular matrix organization, vitamin D binding, TGF-beta signaling pathway, Cartilage oligomeric matrix protein
1.20.5.10.1.1.1.1.15	1fbmE00	Rattus norvegicus, extracellular matrix structural constituent, Focal adhesion, proteinaceous extracellular matrix, fibronectin binding, thrombospondin, ECM-receptor interaction, extracellular matrix organization, vitamin D binding, Cartilage oligomeric matrix protein, TGF-beta 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=1.20.5.10.1.1.1.1

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: 1.20.5.10.1.1.1.1

Classification Lineage (1.20.5.10.1.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 1.20.5.10.1.1.1.1 (15)

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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