Fig. 2
A novel conformation of the polypeptide-binding pocket revealed by BiP-ATP2. a–c Comparison of SBDβ conformations in BiP-ATP2 and BiP-ATP. Ribbon diagrams are drawn for SBDβs from BiP-ATP2 (a, green), BiP-ATP (b, orange; PDB code: 5E84), and their superposition (c). SBDβs were superimposed based on Cαs of β3-β7. Cα atoms of Gly425 and Gly431 are highlighted as blue and purple balls, respectively. The side-chains of Val429 are shown in stick representation. d–f Comparison of the polypeptide-binding sites in BiP-ATP2 (d), BiP-ATP (e), and isolated SBD of BiP (f, PDB code: 5E85). The top panels show the peptide-binding loops, L1,2 and L3,4 (in backbone worm representation). The surface of SBDβs are shown in the bottom panels (negative charge: blue; positive charge: red; and hydrophobic: white. The surfaces with qualitative electrostatic representation were generated by PyMOL using the “generate vacuum electrostatics” function.). The NR peptide bound in the isolated SBD is shown in cyan with the side chains of Leu3, Leu4, and Leu5 (orange) highlighted as stick drawings. BiP-ATP2 and BiP-ATP were superimposed as in a–c; BiP SBD was superimposed to BiP-ATP based on Cαs of β1-β2. The NR peptides in d–e were from f, and the positions were based on superposition. L loop, β β strand
