1Translocation is essential to the anthrax toxin mechanism. Protective antigen, the 2 translocon component of this AB toxin, forms an oligomeric pore with three key clamp sites that 3 aid in the efficient entry of lethal factor or edema factor, the enzymatic components of the toxin, 4 into the cell. LF and EF translocate through the protective antigen pore with the pH gradient 5 between the endosome and the cytosol acting as the driving force. Structural details of the 6 translocation process have remained elusive despite their biological importance. To overcome the 7 technical challenges of studying translocation intermediates, we developed a novel method to 8 immobilize, transition, and stabilize anthrax toxin. Here, we report a cryoEM snapshot of PApore 9 translocating the N-terminal domain of LF. The resulting 3.1 and 3.2 Å structures of the complex 10 trace LFN as it unfolds near the α clamp, translocates through the Φ clamp, and begins to refold in 11 the charge clamp. In addition, helical density inside the β barrel channel suggests LF secondary 12 structural elements begin to refold at the charge clamp site. We conclude the anthrax toxin uses an 13 extended β barrel to efficiently fold the enzymatic payload prior to channel exit. This refolding 14 mechanism has broader implications for pore length of other protein translocating toxins. 15