Photosystem II (PSII), the oxygen-evolving enzyme, consists of 17 trans-membrane and 3 extrinsic membrane proteins. Other subunits bind to PSII during assembly, like Psb27, Psb28, Tsl0063. The presence of Psb27 has been proposed (Zabret et al. 2021; Huang et al. 2021; Xiao et al. 2021) to prevent the binding of PsbJ, a single transmembrane α-helix close to the quinone Q$_B$ binding site. Consequently, a PSII rid of Psb27, Psb28 and Tsl0034 prior to the binding of PsbJ would logically correspond to an assembly intermediate. The present work describes experiments aiming at further characterizing such a ΔPsbJ-PSII, purified from the thermophilic $Thermosynechococcus\ elongatus$ , by means of MALDI-TOF spectroscopy, Thermoluminescence, EPR spectroscopy and UV-visible time-resolved spectroscopy. In the purified ΔPsbJ-PSII, an active Mn$_4$ CaO$_5$ cluster is present in 60-70 % of the centers. In these centers, although the forward electron transfer seems not affected, the Em of the Q$_B$ /Q$_B$$^-$ couple increases by ≥ 120 mV thus disfavoring the electron coming back on Q$_A$ . The increase of the energy gap between Q$_A$ /Q$_A$$^-$ and Q$_B$ /Q$_B$$^-$ could contribute in a protection against the charge recombination between the donor side and Q$_B$ - , identified at the origin of photoinhibition under low light (Keren et al. 1997), and possibly during the slow photoactivation process.