Structural Classifications
SCOP
The SCOP database aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known, including all entries in the Protein Data Bank (PDB). SCOP information was obtained from the database website, more detailed information can be found at http://scop.mrc-lmb.cam.ac.uk/scop/
Classification
Proteins are classified to reflect both structural and evolutionary relatedness. Many levels exist in the hierarchy, but the principal levels are family, superfamily and fold, described below.
- Family: Clear evolutionarily relationship
Proteins clustered together into families are clearly evolutionarily related. Generally, this means that pairwise residue identities between the proteins are 30% and greater. However, in some cases similar functions and structures provide definitive evidence of common descent in the absence of high sequence identity; for example, many globins form a family though some members have sequence identities of only 15%. - Superfamily: Probable common evolutionary origin
Proteins that have low sequence identities, but whose structural and functional features suggest that a common evolutionary origin is probable are placed together in superfamilies. For example, actin, the ATPase domain of the heat shock protein, and hexakinase together form a superfamily. - Fold: Major structural similarity
Proteins are defined as having a common fold if they have the same major secondary structures in the same arrangement and with the same topological connections. Different proteins with the same fold often have peripheral elements of secondary structure and turn regions that differ in size and conformation. In some cases, these differing peripheral regions may comprise half the structure. Proteins placed together in the same fold category may not have a common evolutionary origin: the structural similarities could arise just from the physics and chemistry of proteins favoring certain packing arrangements and chain topologies.
CATH
The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Only X-ray structures solved to resolution better than 4.0 angstroms are considered, together with NMR structures. All non-proteins, models, and structures with greater than 30% “C-alpha only” are excluded from CATH. Protein structures are classified using a combination of automated and manual procedures. CATH information was obtained from the database website, more detailed information can be found at http://www.cathdb.info/
Classification
There are four major levels in this hierarchy: Class, Architecture, Topology (fold family) and Homologous superfamily.
- Class, C-level
Class is determined according to the secondary structure composition and packing within the structure. Three major classes are recognised; mainly-alpha, mainly-beta and alpha-beta. This last class (alpha-beta) includes both alternating alpha/beta structures and alpha+beta structures, as originally defined by Levitt and Chothia (1976). A fourth class is also identified which contains protein domains which have low secondary structure content. - Architecture, A-level
This describes the overall shape of the domain structure as determined by the orientations of the secondary structures but ignores the connectivity between the secondary structures. It is currently assigned manually using a simple description of the secondary structure arrangement e.g. barrel or 3-layer sandwich. Reference is made to the literature for well-known architectures (e.g the beta-propellor or alpha four helix bundle). - Topology (Fold family), T-level
Structures are grouped according to whether they share the same topology or fold in the core of the domain, that is, if they share the same overall shape and connectivity of the secondary structures in the domain core. Domains in the same fold group may have different structural decorations to the common core. Some fold groups are very highly populated particularly within the mainly-beta 2-layer sandwich architectures and the alpha-beta 3-layer sandwich architectures. - Homologous Superfamily, H-level
This level groups together protein domains which are thought to share a common ancestor and can therefore be described as homologous. Similarities are identified either by high sequence identity or structure comparison using SSAP.
