Secreted and membrane proteins are translocated across/into cell membranes via a protein-conducting channel (PCC). We present a cryo-EM reconstruction of the E. coli PCC, SecYEG, complexed with the ribosome and a signal anchor containing nascent chain, showing mRNA, three tRNAs, the nascent chain, and detailed features of both a translocating PCC and a second, non-translocating PCC bound to mRNA hairpins. The translocating PCC forms connections with ribosomal RNA hairpins on two sides and ribosomal proteins at the back, leaving a frontal opening. Normal mode-based flexible fitting of the archaeal SecYEβ structure into the PCC EM densities favors a front-to-front arrangement of two SecYEG complexes in the PCC, and supports channel formation by the opening of two linked SecY halves during polypeptide translocation. Based on our observation in the translocating PCC of two segregated pores with different degrees of access to bulk lipid, we propose a model for co-translational protein translocation.