How to annotate complexes in GO-CAM

When complexes are involved in specific activities, several options are available in GO-CAM to represent them.

1. The subunit that carries the molecular activity is known:

In that case, the complex is not described and the activity(ies) is represented by the specific protein (s) carrying the activity.

Ex:

In this example, all the proteins in the E3 ligase complex have a defined and precise activity. Therefore, they are all displayed in the model. In this case, the scaffold activity is usually represented first, activating subsequent activities from the complex.

1. The subunit which carries the molecular activity is not known:

If the precise subunit carrying the activity is not known, we can use the GO accession for the complex.

Ex: Ragulator complex (GO:0071986): Ragulator is comprised of the membrane anchor subunit LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4 and LAMTOR5.

![A screenshot of a computer

Description automatically generated](data:image/png;base64...)

In this example LAMTOR1 activity is known (protein-membrane adaptor activity) but the protein that carries the guanyl-nucleotide exchange factor activity is not known, therefore we use the complex ID from GO in this situation.

1. If the activity is shared by several proteins

EX: Heterodimeric receptor where both activities are important for activity.