The first picture of a protein shown in a publication is often a cartoon of the secondary structure . Domains are whatever the authors define them as. In the case of UvrB, we highlighted the parts similar to other helicases in yellow and red, while the green, blue and cyan elements were novel. We did try to separate the protein into parts with separate hydrophobic cores along sensible boundaries, but there is mostly no experimental evidence. However, the blue domain is a real domain in the sense that it was deleted in a protein variant that retained function (except UvrA-binding, which is through the blue domain). In a different study, the cyan element was deleted, and again, the remainder of the protein folded properly (but no longer bound tightly to DNA, which is via the cyan hairpin loop).
select protein; cartoon; color gold;
select 415-600; color red;
select 157-244; color blue;
select 244-324, 349-378; color lime;
select 91-116; color cyan;
To show where negatively or positively charged molecules are bound, 2D-figures sometimes show surfaces colored by an electrostatic potential calculated from the point charges on Asp, Glu, Arg, Lys and - if the charge state is known - His. The common color scheme is blue for positive and red for negative potential (corresponding nicely to the CPK color scheme with blue nitrogen atoms - carrying a positive formal charge - and red oxygen atoms - carrying a negative formal charge). A quick and simple approximation in Jmol is to show the molecule as spacefill, and . (You could also just color the side chain oxygen and nitrogen atoms, but you then ignore charges of disordered atoms missing in the model but present in the protein.) The UvrB protein shown does not exhibit any obvious regions of positive or negative charges.
select protein; spacefill 100%; color silver;
select (arg, lys, his) AND sidechain; color blue;
select (arg, lys, his) AND sidechain; color blue;
To show evolutionary
, we use data from ConSurf.
157-244 blue
415-600 red
349 - 378 lime
244 - 324 lime
91 - 116 cyan
