AlphaFold Fetch

AlphaFold is an artificial intelligence method for predicting protein structures. With the AlphaFold tool or command, ChimeraX can search for and load predicted structures from the freely available AlphaFold Database, automatically coloring them by confidence value:

• 100 to 90 – high accuracy
• 90 to 70 – backbone accuracy
• 70 to 50 – low confidence, caution
• 50 to 0 – should not be interpreted, may be disordered

The figure shows the predicted structure of UniProt entry TOM40_HUMAN, a channel protein needed to import other proteins into mitochondria. See the command file tom40.cxc for fetching data and other setup (background color, etc.).

Opening a sequence from UniProt also opens a dialog in which its annotations or “features” can be clicked to highlight those regions in both the sequence and the associated 3D structure. The low-confidence part of this structure (orange and red) maps to compositionally biased and likely disordered regions near the N-terminus of the sequence.

Potassium Channel-Calmodulin Complex

KCNQ1 is the pore-forming subunit of a cardiac potassium channel. It binds to calmodulin, and mutations in either of these proteins can cause congenital long QT syndrome, a dangerous propensity for irregular heartbeats. In the image, a structure of the KCNQ1/calmodulin complex (PDB 5vms) has been assembled into the native tetrameric form with the sym command. The view is from the cytoplasmic side, with KCNQ1 shown as surfaces, calmodulin as cartoons, and calcium ions as balls. A pastel palette from ColorBrewer has been used to color the surfaces, darkened with color modify for the cartoons, and “rotated” 45° in hue for the ions. See the command file colormod.cxc.

More images...