Integration of macromolecular complex data into the Saccharomyces Genome Database

Abstract

Proteins seldom function individually. Instead, they interact with other proteins or nucleic acids to form stable macromolecular complexes that play key roles in important cellular processes and pathways. One of the goals of Saccharomyces Genome Database (SGD; www.yeastgenome.org) is to provide a complete picture of budding yeast biological processes. To this end, we have collaborated with the Molecular Interactions team that provides the Complex Portal database at EMBL-EBI to manually curate the complete yeast complexome. These data, from a total of 589 complexes, were previously available only in SGD's YeastMine data warehouse (yeastmine.yeastgenome.org) and the Complex Portal (www.ebi.ac.uk/complexportal). We have now incorporated these macromolecular complex data into the SGD core database and designed complex-specific reports to make these data easily available to researchers. These web pages contain referenced summaries focused on the composition and function of individual complexes. In addition, detailed information about how subunits interact within the complex, their stoichiometry and the physical structure are displayed when such information is available. Finally, we generate network diagrams displaying subunits and Gene Ontology annotations that are shared between complexes. Information on macromolecular complexes will continue to be updated in collaboration with the Complex Portal team and curated as more data become available.

Figure 1

Schematic of macromolecular complex data object. Data for macromolecular complexes were expertly collected and curated from published literature. Each box represents a data type stored in the database. Arrows indicate how data is related to the complex object.

Figure 2

Summary and diagram sections of SOD1-CCS1 superoxide dismutase heterodimer page. Summary section that describes the function and composition of the SOD1-CCS1 superoxide dismutase complex. Individual interactions between subunits are shown in the Complex Diagram section. Complex diagrams can be downloaded as .png files. Complete page at www.yeastgenome.org/complex/CPX-2267.

Figure 3

Network diagram of SOD1-CCS1 superoxide dismutase heterodimer page. GO annotations and complex subunits that are shared between the focus complex and other complexes are shown as a network. Users can select to see shared GO terms or shared subunits individually or both. Images can be downloaded as .png files.