Coloring by Sequence Conservation

Atomic structures, including cartoons and molecular surfaces, can be colored by the conservation in an associated multiple sequence alignment. The figure shows a structure of the β₂-adrenergic receptor signaling complex (PDB 3sn6) with receptor cartoon colored blue→white→red from least conserved to most conserved. The β₂-adrenergic receptor is a member of the class A G-protein-coupled receptor superfamily. Conservation was calculated from a superfamily alignment from PASS2 using the entropy-based measure from AL2CO (included with ChimeraX courtesy of Pei and Grishin). The sequence alignment and step-by-step instructions for making this image are given in the Coloring by Sequence Conservation tutorial.

Cyclodextrin Pore

The outer-membrane protein CymA admits bulky molecules into the periplasmic space of Klebsiella oxytoca. Here, CymA (PDB 4d5d chain A) is depicted in a style reminiscent of a diagnostic X-ray, with transparent molecular surface and β-strand “ribs” in white. The protein has ingested α-cyclodextrin (top) and β-cyclodextrin (bottom), bound at the entry site and near the exit, respectively. Cyclodextrin carbon atoms are shown in blue-gray and oxygen atoms in brick red. For image setup, see the command file xray.cxc.

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