The body in the box (5)
I believe the answer is:
trunk
I believe this clue is a double definition.
'the body' is the first definition.
(synonyms)
'the box' is the second definition.
(thesaurus)
'in' acts as a link.
(Other definitions for trunk that I've seen before include "Proboscis" , "main part of plane" , "Large storage box" , "Baggage item" , "Main body - chest" .)