How to structure a sharepoint site for a college department with different disciplines?

I am tasked with creating a sharepoint site for the IT department of a College. The IT department is made up of three disciplines, Engineering, IT and Environment. Each discipline wants to move their research data to SharePoint, but not share it with other discipline members. However, some Engineering and IT units are part of multiple courses across the 2 disciplines, but Environment does not overlap with other disciplines. How do I design the site and create a site hierarchy and permission groups?