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SCOP, structural classification of proteins

Levels of hierarchy:

1. Domain

2. Family = similarities in structure, sequence and function implies common evolutionary origin

3. superfamilies = similar structure and function, but evidence for evolutionary relationship is suggestive but not compelling

4. Fold = superfamilies with a common folding topology for at least a central portion of the structure

5. Class = a, b, a+b, a/b, multi domain proteins, membrane and cell surface proteins, small proteins without a or b:

1. All alpha proteins
2. All beta proteins 
3. Alpha and beta proteins (a/b) 
   Mainly parallel beta sheets (beta-alpha-beta units)
4. Alpha and beta proteins (a+b) 
   Mainly antiparallel beta sheets (segregated alpha and beta regions)
5. Multi-domain proteins (alpha and beta)
   Folds consisting of two or more domains belonging to different classes
6. Membrane and cell surface proteins and peptides 
   Does not include proteins in the immune system
7. Small proteins 
   Usually dominated by metal ligand, heme, and/or disulfide bridges

          Others:

• Coiled coil proteins 
  Not a true class
• Low resolution protein structures 
  Not a true class
• Peptides 
  Peptides and fragments. Not a true class
• Designed proteins 
  Experimental structures of proteins with essentially non-natural sequences. Not a true class

Definition on the SCOP website (taken from http://scop.mrc-lmb.cam.ac.uk/scop/intro.html on October 13, 2002):

• 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 absense 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.

what are the numbers of entries in each of these hierarchies? Where does the number of 7000 folds come from?

Current statistics (as of October 13, 2002):