S100 Family: 3.40.190.10.8.1.1.1

Representative domain: 1ryoA02

Classification Lineage (3.40.190.10.8.1.1.1)

CATH Code	Level Description	Links
3	Alpha Beta
3.40	3-Layer(aba) Sandwich
3.40.190	D-Maltodextrin-Binding Protein; domain 2
3.40.190.10	Periplasmic binding protein-like II	Gene3D
3.40.190.10.8
3.40.190.10.8.1
3.40.190.10.8.1.1
3.40.190.10.8.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	16

Non-Redundant Representatives (16)
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 3.40.190.10.8.1.1.1 (16)

CATH code	Domain ID	Keywords
3.40.190.10.8.1.1.1.1	1ryoA02	protein binding, early endosome, Serotransferrin, recycling endosome, apical plasma membrane, Homo sapiens, coated pit, late endosome, endocytic vesicle, perinuclear region of cytoplasm, basal plasma membrane
3.40.190.10.8.1.1.1.2	1a8eA02	protein binding, early endosome, Serotransferrin, recycling endosome, apical plasma membrane, Homo sapiens, coated pit, late endosome, endocytic vesicle, perinuclear region of cytoplasm, basal plasma membrane
3.40.190.10.8.1.1.1.3	1a8fA02	coated pit, late endosome, endocytic vesicle, perinuclear region of cytoplasm, basal plasma membrane, protein binding, early endosome, Serotransferrin, recycling endosome, apical plasma membrane, Homo sapiens
3.40.190.10.8.1.1.1.4	1oqgA02	early endosome, protein binding, Serotransferrin, apical plasma membrane, recycling endosome, Homo sapiens, coated pit, endocytic vesicle, late endosome, basal plasma membrane, perinuclear region of cytoplasm
3.40.190.10.8.1.1.1.5	1n84A02	coated pit, late endosome, endocytic vesicle, perinuclear region of cytoplasm, basal plasma membrane, protein binding, early endosome, Serotransferrin, recycling endosome, apical plasma membrane, Homo sapiens
3.40.190.10.8.1.1.1.6	1fqfA02	apical plasma membrane, recycling endosome, Homo sapiens, early endosome, protein binding, Serotransferrin, basal plasma membrane, perinuclear region of cytoplasm, coated pit, endocytic vesicle, late endosome
3.40.190.10.8.1.1.1.7	1n7xA02	Serotransferrin, protein binding, early endosome, Homo sapiens, recycling endosome, apical plasma membrane, late endosome, endocytic vesicle, coated pit, perinuclear region of cytoplasm, basal plasma membrane
3.40.190.10.8.1.1.1.8	1bp5A02	Serotransferrin, early endosome, protein binding, Homo sapiens, apical plasma membrane, recycling endosome, endocytic vesicle, late endosome, coated pit, basal plasma membrane, perinuclear region of cytoplasm
3.40.190.10.8.1.1.1.9	1bp5B02	protein binding, early endosome, Serotransferrin, recycling endosome, apical plasma membrane, Homo sapiens, coated pit, late endosome, endocytic vesicle, perinuclear region of cytoplasm, basal plasma membrane
3.40.190.10.8.1.1.1.10	1bp5C02	coated pit, late endosome, endocytic vesicle, perinuclear region of cytoplasm, basal plasma membrane, protein binding, early endosome, Serotransferrin, recycling endosome, apical plasma membrane, Homo sapiens
3.40.190.10.8.1.1.1.11	1bp5D02	protein binding, early endosome, Serotransferrin, recycling endosome, apical plasma membrane, Homo sapiens, coated pit, late endosome, endocytic vesicle, perinuclear region of cytoplasm, basal plasma membrane
3.40.190.10.8.1.1.1.12	1n7wA02	late endosome, endocytic vesicle, coated pit, perinuclear region of cytoplasm, basal plasma membrane, Serotransferrin, protein binding, early endosome, Homo sapiens, recycling endosome, apical plasma membrane
3.40.190.10.8.1.1.1.13	2havA02	apical plasma membrane, recycling endosome, Homo sapiens, early endosome, protein binding, Serotransferrin, basal plasma membrane, perinuclear region of cytoplasm, coated pit, endocytic vesicle, late endosome
3.40.190.10.8.1.1.1.14	2havB02	Serotransferrin, protein binding, early endosome, Homo sapiens, recycling endosome, apical plasma membrane, late endosome, endocytic vesicle, coated pit, perinuclear region of cytoplasm, basal plasma membrane
3.40.190.10.8.1.1.1.15	1btjA02	endocytic vesicle, late endosome, coated pit, basal plasma membrane, perinuclear region of cytoplasm, Serotransferrin, early endosome, protein binding, Homo sapiens, apical plasma membrane, recycling endosome
3.40.190.10.8.1.1.1.16	1btjB02	perinuclear region of cytoplasm, basal plasma membrane, coated pit, late endosome, endocytic vesicle, recycling endosome, apical plasma membrane, Homo sapiens, protein binding, early endosome, Serotransferrin

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=3.40.190.10.8.1.1.1

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: 3.40.190.10.8.1.1.1

Classification Lineage (3.40.190.10.8.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 3.40.190.10.8.1.1.1 (16)

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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