Its box is of bone (5)

I believe the answer is:

brain

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'bone' is the definition.
The answer and definition can be both body parts as well as being singular nouns.
Perhaps there's an association between them I don't understand?

I can't explain the rest of the clue.

Can you help me to learn more?

(Other definitions for brain that I've seen before include "Clever person" , "Haemorrhaging of talent" , "Mastermind" , "The grey matter" , "Hit hard; intellect" .)

I've seen this clue in the Evening Standard.

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