Rodent confined in church box (5)
I believe the answer is:
crate
'box' is the definition.
(crate is a kind of box)
'rodent confined in church' is the wordplay.
'rodent' becomes 'rat' (rat is a kind of rodent).
'confined in' means one lot of letters goes inside another.
'church' becomes 'CE' (abbreviation for Church of England).
'rat' going within 'ce' is 'CRATE'.
(Other definitions for crate that I've seen before include "Old soldiers might be found in this" , "heap" , "Wooden container" , "Wooden box" , "Large box" .)