The Immunoglobulin (Ig) fold is the most common protein structure unit in the human proteome and is involved in many cellular signaling pathways. NCBI along with researchers at the National Cancer Institute and California State University, Northridge have developed a universal reference numbering scheme for Ig folds, now available in the iCn3D structure viewer, to help you compare and analyze proteins with this common fold. iCn3D can also automatically detect Ig domains in structures by comparing them to a library of diverse Ig template structures.
Check out the example below to see a graphical display of the Ig fold in a human T-cell receptor CD8 structure and our new numbering scheme in iCn3D.
Figure 1. iCn3D display of the human T-cell receptor CD8 structure (1CD8) showing Ig fold detection and reference numbers. The top panel (A) shows the 3D rendering of the structure. The automatically detected Ig domain is colored by Ig strand designation. The bottom panel shows detailed reference numbers in the line “IgStRAnd Ref. No.” An anchor residue in each strand is assigned a 4-digit number of the form ##50. For example, the reference number 1550 is the anchor residue for the “A” strand. The residues before and after the anchor residue are assigned as the preceding and following integers: ##48, ##49, and ##51, ##52, etc.
The “IgStrand” reference numbers also allow you to compare the interactions formed by different Ig domains. Figure 2 shows the interactions between two IgV domains in the alignment of two structures. The display allows you to see where the interactions are the same and where they are different.
Figure 2. iCn3D display of an alignment of two structures showing the interactions between two IgV domains. A) CD96 interacting with nectin-like protein-5 (necl-5) (6ARQ). B) TIGIT interacting with necl-5 (3UDW). Interactions between the IgV domains in the alignment are mapped using IgStrand reference numbers. Different types of interactions are assigned specific colors: hydrogen bonds, contacts, and π-stacking are colored in green, gray, and blue, respectively. The IgStrand reference numbers highlight the differences between these two structures shown in panel C.
Learn more
Check out our bioRxiv preprint for more details.
Stay up to date
Follow us on social @NCBI and join our mailing list to keep up to date with iCn3D and other NCBI news.
Questions?
Feel free to contact our help desk at info@ncbi.nlm.nih.gov if you have any questions or concerns.