The protons in the lumen come from three primary sources.
*Photolysis by photosystem II oxidises water to oxygen, protons and electrons in the lumen.
*The transfer of electrons from photosystem II to plastoquinone during non-cyclic electron transport consumes two protons from the stroma. These are released in the lumen when the reduced plastoquinol is oxidized by the cytochrome b6f protein complex on the lumen side of the thylakoid membrane. From the plastoquinone pool, electrons pass through the cytochrome b6f complex. This integral membrane assembly resembles cytochrome bc1.
*The reduction of plastoquinone by ferredoxin during cyclic electron transport also transfers two protons from the stroma to the lumen.
The proton gradient is also caused by the consumption of protons in the stroma to make NADPH from NADP+ at the NADP reductase.