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.

Neuraminidase Flowers

Influenza neuraminidase is an enzyme that promotes the spread of influenza virus among host cells. It is the target of oseltamivir and related antiviral drugs. The image shows tetramers of neuraminidase (PDB 3k3a) styled as flowers. Three tetramers are in different shades of pink, with a central metal ion in white and nearby residues in yellow, and a fourth tetramer is colored green to resemble leaves. Each monomer or “petal” is a six-bladed β-propeller. For image setup other than orientation, see the command file flowers.cxc. The Chimera Image Gallery includes a similar image.

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