Primate guarding small part of church (4)
I believe the answer is:
apse
'part of church' is the definition.
(part of a church building)
'primate guarding small' is the wordplay.
'primate' becomes 'ape' (large primate).
'guarding' indicates putting letters inside.
'small' becomes 's' (abbreviation - e.g. clothes size).
'ape' going around 's' is 'APSE'.
(Other definitions for apse that I've seen before include "where praetor sat" , "Strange peas in the church recess" , "Peas (anag) -- part of a church" , "Recess at eastern end of a church" , "Church recess with domed or arched roof" .)