S100 Family: 1.25.40.180.5.1.1.1

Representative domain: 3feyA02

Classification Lineage (1.25.40.180.5.1.1.1)

CATH Code	Level Description	Links
1	Mainly Alpha
1.25	Alpha Horseshoe
1.25.40	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
1.25.40.180		Gene3D
1.25.40.180.5
1.25.40.180.5.1
1.25.40.180.5.1.1
1.25.40.180.5.1.1.1

Summary of Non-Redundant Representatives


-	-	-	-	-	-	-	-	11

Non-Redundant Representatives (11)
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 1.25.40.180.5.1.1.1 (11)

CATH code	Domain ID	Keywords
1.25.40.180.5.1.1.1.1	3feyA02	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, protein binding, Nuclear cap-binding protein subunit 1, ribonucleoprotein complex, nuclear cap-binding protein subunit 1, mRNA cap binding complex, Homo sapiens, regulation of translational initiation, mRNA cleavage, mRNA export from nucleus, mRNA capping, RNA cap binding, positive regulation of mRNA 3'-end processing, Spliceosome
1.25.40.180.5.1.1.1.2	1h2vC02	Spliceosome, positive regulation of mRNA 3'-end processing, RNA cap binding, mRNA capping, mRNA export from nucleus, nuclear cap-binding protein subunit 1, mRNA cleavage, Homo sapiens, regulation of translational initiation, mRNA cap binding complex, Nuclear cap-binding protein subunit 1, ribonucleoprotein complex, protein binding, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
1.25.40.180.5.1.1.1.3	1h6kA02	nuclear cap-binding protein subunit 1, mRNA cap binding complex, mRNA cleavage, Homo sapiens, regulation of translational initiation, protein binding, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, Nuclear cap-binding protein subunit 1, ribonucleoprotein complex, Spliceosome, RNA cap binding, mRNA export from nucleus, mRNA capping, positive regulation of mRNA 3'-end processing
1.25.40.180.5.1.1.1.4	1h6kB02	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, protein binding, Nuclear cap-binding protein subunit 1, ribonucleoprotein complex, nuclear cap-binding protein subunit 1, mRNA cap binding complex, Homo sapiens, regulation of translational initiation, mRNA cleavage, mRNA capping, mRNA export from nucleus, RNA cap binding, positive regulation of mRNA 3'-end processing, Spliceosome
1.25.40.180.5.1.1.1.5	1h6kC02	RNA cap binding, mRNA export from nucleus, mRNA capping, positive regulation of mRNA 3'-end processing, Spliceosome, protein binding, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, ribonucleoprotein complex, Nuclear cap-binding protein subunit 1, mRNA cap binding complex, mRNA cleavage, Homo sapiens, regulation of translational initiation, nuclear cap-binding protein subunit 1
1.25.40.180.5.1.1.1.6	1n52A02	ribonucleoprotein complex, Nuclear cap-binding protein subunit 1, protein binding, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, mRNA cleavage, Homo sapiens, regulation of translational initiation, mRNA cap binding complex, nuclear cap-binding protein subunit 1, positive regulation of mRNA 3'-end processing, RNA cap binding, mRNA capping, mRNA export from nucleus, Spliceosome
1.25.40.180.5.1.1.1.7	1h2tC02	positive regulation of mRNA 3'-end processing, RNA cap binding, mRNA capping, mRNA export from nucleus, Spliceosome, ribonucleoprotein complex, Nuclear cap-binding protein subunit 1, protein binding, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, mRNA cleavage, Homo sapiens, regulation of translational initiation, mRNA cap binding complex, nuclear cap-binding protein subunit 1
1.25.40.180.5.1.1.1.8	1h2uA02	protein binding, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, ribonucleoprotein complex, Nuclear cap-binding protein subunit 1, mRNA cap binding complex, mRNA cleavage, Homo sapiens, regulation of translational initiation, nuclear cap-binding protein subunit 1, RNA cap binding, mRNA export from nucleus, mRNA capping, positive regulation of mRNA 3'-end processing, Spliceosome
1.25.40.180.5.1.1.1.9	1h2uB02	positive regulation of mRNA 3'-end processing, mRNA capping, mRNA export from nucleus, RNA cap binding, Spliceosome, ribonucleoprotein complex, Nuclear cap-binding protein subunit 1, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, protein binding, Homo sapiens, regulation of translational initiation, mRNA cleavage, mRNA cap binding complex, nuclear cap-binding protein subunit 1
1.25.40.180.5.1.1.1.10	1n54A02	mRNA cap binding complex, mRNA cleavage, Homo sapiens, regulation of translational initiation, nuclear cap-binding protein subunit 1, ribonucleoprotein complex, Nuclear cap-binding protein subunit 1, protein binding, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, Spliceosome, positive regulation of mRNA 3'-end processing, RNA cap binding, mRNA capping, mRNA export from nucleus
1.25.40.180.5.1.1.1.11	3fexA02	Spliceosome, mRNA capping, mRNA export from nucleus, RNA cap binding, positive regulation of mRNA 3'-end processing, mRNA cap binding complex, Homo sapiens, regulation of translational initiation, mRNA cleavage, nuclear cap-binding protein subunit 1, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, protein binding, ribonucleoprotein complex, Nuclear cap-binding protein subunit 1

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=1.25.40.180.5.1.1.1

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: 1.25.40.180.5.1.1.1

Classification Lineage (1.25.40.180.5.1.1.1)

Summary of Non-Redundant Representatives

What is a Non-Redundant Representative?

S100 Count Entries in S100 Family 1.25.40.180.5.1.1.1 (11)

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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