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One difference from the standard C2-set connectivity is the absence of strand a from the outer sheet of the E2 β sandwich, which could be due to disorder or to truncation of E2 VR2 in the construct. A more important difference is the absence of a canonical disulfide connecting outer and inner sheets at strands b and f that is present in most Ig folds, although observed together with C2-set strand connectivity in some bacterial, actinoxanthine-like, and fibronectin III-like domains comprising the C3, C4, and FN3 sets. However, the E2 β sandwich has disulfides linking the loop before strand b with strand g (residues 494 to 564) and strand c with strand f (508 to 552), which are typically observed in the C2 set but not for the C3, C4, or Fn3 sets. This unique disulfide system found in the E2 β sandwich may have constrained the rotational angle between inner and outer sheet strands to be nearly parallel, rather than the -30° offset commonly observed in Ig folds. Together, these features suggest the E2 β sandwich is similar to the C2 set but with differences such as lack of strand a, lack of disulfide connection between strands b and f, and lack of -30° offset between front and back sheets that prevent finding significant matches with equivalent strand connectivity to other structures in the Protein Data Bank (PDB) using structural homology programs DALI and FATCAT (15).
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2 because of the kifunensine treatment during protein production.
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This calculation was made from searching the International Immunogenetics Information System (IMGT) database on 27 March 2013. There were n = 8832 IGHD germline genes in the database, of which 1514 contained the disulfide motif.
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