IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes
Fig 5
A) IgStrand numbers for anchors and additional key residues in important IgV domains Definitions for Classical Strands (1000’s), Non-classical Strands (100’s) with Anchor numbers (50s). Residue types are shown for well-known IgV examples as in antibodies where sheet 1 is composed of strands ABED and sheet 2 (A’)GFCC’(C”). The A strand anchor residue is given the number 1550, where it is the first strand (A) on Sheet 1. A’ strand anchor is given the number 1850 it is the second half of the A strand swaps to Sheet 2 adjacent to the G strand in parallel. The B strand anchor is 2550. C strand anchor is 3550 and is on Sheet 2. C’ strand anchor is 4550 and is on Sheet 2. C” strand anchor is 5550 on Sheet 2, but it can swap to Sheet 1. D strand anchor is 6550. The E strand anchor is 7550. The F strand anchor is 8550. The G strand anchor is 9550. Additional, non-classical strands can also appear in Ig-extended domains. This is taken into account by the second digit, for example the anchor of the strand appearing before the A strand (A- strand) will have the IgStrand number 1450, while the anchor of a strand A+ after the A strand will be 1650, and for a G+ strand appearing after a G strand similarly 9650. The anchors form a network. B) shows the extensive residue interaction network between the anchors core and residues in all strands of the fold. C) shows sidechain and backbone representations of all anchors with respect to the overall fold. D) shows the positions and backbone connections of the anchors in the GFCC’C” Sheet 2. E) shows D 6550 and E 7550 strand anchors vs. A 1550 and B 2550 anchors on the ABED Sheet 1. F) shows the interaction of A strand anchor 1550 with the backbone of 8550, forming the signature bulge in the G strand of IgVs. G) shows the position of 1850 in the A’ strand with respect to the F and G strand residues. (PDBid used: 5ESV_H for heavy chain variable domain).