Usually these stories involve ensemble casts; it's not immediately clear who the protagonist is. Yet there is one character who, through action or theme, "oversees" the movement of the story. The structural development of these ensemble stories embraces one of two strategies.
In the first, in movies like Dead Poet's Society or Cocoon, a group of people in the same place and circumstances tell the story. Teacher and students at a school or the residents of a retirement home interact as a group, and within this ensemble the story is told. But the story is driven by the decisions of one of them. Within the ensemble is a protagonist, though the role sometimes may vary, a shifting protagonist if you will.
In the second strategy, the ensemble characters are not grounded in common place and time but are related by theme. Examples are movies like Magnolia and Traffic. In the latter, for example, we have three major story threads, which physically overlap in minor ways but which are thematically related in much more important ways: the drug czar and his world, including his addicted daughter; a good Mexican cop and his world; and a good American drug agent and his world. Here I would call the drug czar, played by Michael Douglas, the protagonist (this character has the thematic over-view) but the story unfolds by telling these 3 threaded stories in a rhythm that moves between them.
Each thread in Traffic has its dramatic structure, its beginning, middle and end. The overall story is then a sequence that moves between these threads. Imagine these threads are called A, B and C and the sequence outline of each is called A1, A2 ... A10, B1 ... B10 and C1 ... C10. The story movement of the whole then becomes something like A1, B1, A2, C1, C2, B2, A3 and so on.
Beginners sometimes confuse chronology with structure. A story does not have to be told chronologically in order to have dramatic structure, and there are many examples that prove this (for example, Nixon).
Consider the unusual movie Memento (2000), which has repetitive, non-chronological scenes and is presented as something of a puzzle. At first, it may seem that this story has no traditional dramatic structure at all. But dramatic structure depends on the order of information presented to the audience. Once this is understood, Memento's "traditional" 3-act structure becomes clear: a hook in which the protagonist "has a condition"; a complication in which this is identified as very short-term memory loss; a first act plot point in which we understand he is on a mission of revenge, to find and kill the man who raped and murdered his wife; a midpoint in which a woman who has been helping him is revealed to be, in fact, using him; and an end of act two low point in which we realize the man is trapped to continue his search forever. In a sense, here it is the audience as well as the non-understanding protagonist who has a journey. All the same, 3-act dramatic movement is in place.
The bottom line is creating in the audience the question What happens next? These creative structures do not violate 3-act storytelling but extend its power and possibilities.