Much of the knowledge on the structure of the SecY/Sec61α pore comes from an X-ray crystallography structure of its
archaeal version. The large SecY subunit consists of two halves, trans-membrane segments 1-5 and trans-membrane segments 6-10. They are linked at the extracellular side by a loop between trans-membrane segments 5 and 6. SecY can open laterally at the front (lateral gate). SecE is a single spanning membrane protein in most species. It sits at the back of SecY, wrapping around the two halves of SecY. Secβ (SecG) is not essential. Its sits on the side of SecY and makes only few contacts with it. In a side view, the channel has an hourglass shape, with a cytoplasmic funnel that is empty, and an extracellular funnel that is filled with a little helix, called the plug. In the middle of the membrane is a construction, formed from a pore ring of four hydrophobic
amino acids that project their side chains inwards. During protein translocation, the plug is moved out of the way, and a polypeptide chain is moved from the cytoplasmic funnel, through the pore ring, the extracellular funnel, into the extracellular space. Hydrophobic segments of membrane proteins exit sideways through the lateral gate into the lipid phase and become membrane-spanning segments. Eukaryotic translocon uses BiP. The structure of human Sec61 is resolved at 3.84 Å by
cryo-EM in 2020, together with the rest of the co-translational
translocon including the ribosome. The archaeal translocon is less understood. It might use
SecDF-
YajC and
YidC like bacteria, as homologs have been found. An ATPase is yet to be identified. ==Species-specifics==