a Sequence alignment of GlSec61α from G. lamblia Assemblage A isolate WB with orthologous sequences from S. cerevisiae, A. thaliana, H. sapiens, C. lupus, S. scrofa, C. hominis, P. falciparum, T. gondii, L. major, T. brucei, E. coli, M. jannaschii, T. thermophilus and P. furiosus. The secondary structure elements have been marked below the alignment, with spirals representing α-helices, arrows representing β-strands and lines representing intervening loops. Only the transmembrane helices have been numbered. The downward pointing red arrow marks the conserved arginine (R) required for interaction with ribosome while the functionally-equivalent lysine (K) residue in the putative GlSec61α has been highlighted with a black box. b Tertiary structure of a section of GlSec61α obtained by homology modeling based on 2WWB (i, ii and iii) and 3J7Q (iv, v and vi). Each of the homology modeled structures underwent molecular dynamic simulation for 30 ns, with (iii and vi) or without (ii and v) docked RNA. The side chains of residues K426 and E414 are shown. To indicate the orientation of the loop 8/9, two residues on either side of K426 have been marked (424-dark blue, 425-light blue, 427-amber and 428-red).