The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures

Abstract

The Structural Classification of Proteins (SCOP) database is a classification of protein domains organised according to their evolutionary and structural relationships. We report a major effort to increase the coverage of structural data, aiming to provide classification of almost all domain superfamilies with representatives in the PDB. We have also improved the database schema, provided a new API and modernised the web interface. This is by far the most significant update in coverage since SCOP 1.75 and builds on the advances in schema from the SCOP 2 prototype. The database is accessible from http://scop.mrc-lmb.cam.ac.uk.

Figure 1.

Trivial protein relationships in the current SCOP classification. These are exemplified by TrmB-like family of transcriptional regulators (SCOP ID 4000158) that are related to protein domains members of the SCOP ‘Winged helix DNA-binding domains’ superfamily (SCOP ID 3000034). Their classification is very similar to the SCOP 1.75 classification. (A) SCOP family page showing details of the node classification and annotation. A clickable ancestry chart displays the hierarchical relations between different nodes and allows navigating and exploring their classification. At the bottom of the page all relevant information about the constituent family domains is listed. (B) SCOP superfamily domain page of a member of ‘Winged helix DNA-binding domains’ superfamily (SCOP ID 3000034) showing details of its sequence and structure. On the sequence viewer both, the family and superfamily domains are displayed and demonstrate their differences. The superfamily domain is smaller than the family domain as it defines the evolutionary conserved core of this superfamily.

Figure 2.

SCOP family that comprises two domains each of which a member of a distinct superfamily. The glycoside hydrolase family 64 (SCOP ID 4004596) domain spans over two structural domains, one of which belongs to the ‘Osmotin/thaumatin-like’ superfamily (SCOP ID 3001451) and the other, of a novel fold, classified into its own superfamily (SCOP ID 3002495) (23).

Figure 3.

SCOP family with a fold distinct from the fold of the other superfamily domains. The ‘PqqD-like’ family of PQQ biosynthesis enzymes belongs to the superfamily of ‘Winged helix DNA-binding domains’ (SCOP ID 3000034) but it has evolved a globally different fold from the other superfamily members.