( It ( ( is ( in ( ( the nucleus ) ( where ( ( the ( ( protons and ) neutrons ) ) ( are located ) ) ) ) ) ) . ) )
(ROOT (S (NP (PRP It)) (VP (VBZ is) (PP (IN in) (NP (NP (DT the) (NN nucleus)) (SBAR (WHADVP (WRB where)) (S (NP (DT the) (NNS protons) (CC and) (NNS neutrons)) (VP (VBP are) (VP (VBN located)))))))) (. .)))
It is in the nucleus where the protons and neutrons are located.
(ROOT (S (NP (NNS Protons) (CC and) (NNS neutrons)) (VP (VBP are) (VP (VBN located) (PP (IN in) (NP (DT the) (JJ central) (NN nucleus))))) (. .)))