3D Protein model

A protein structure from PDBe (Protein Data Bank, Europe) for the selected transcript is shown in a LiteMol viewer.

A protein may have multiple structures in the PDBe, so you can choose from a drop down at the top of the viewer which one you want to see. A maximum of ten structures are listed, which provide the most coverage of the protein sequence and have the highest quality score in the PDBe, with the default selection being the highest scoring of these. These may include protein complexes and the protein bound to a ligand.

The display uses LiteMol controls to navigate:

(This video was adapted from one provided by PDBe.)

The menu on the right-hand side allows you to plot Ensembl features onto the view, including variants, exons and protein domains. Click on the eye icon to plot the features onto the sequence. Click on the plus icon to expand the menu to see the features of that type available. This allows the features to be plotted individually, and also shows the colour codes used in the display and the protein coordinates of the features.

Missense variants can be plotted onto the structure with their SIFT and PolyPhen predictions. The expanded menu also shows their amino acid changes and scores.

Controls at the top right of the image allow you to change the protein view. The cog icon allows you to change field of vision and background colour. The tools icon allows you to change the way the molecules are rendered, such as hiding water and ligands, changing the colour of the peptide chain and changing the peptide between cartoon, line, ball and stick, VDV or surface view. When you open the tools icon, this will open a menu at the bottom of the view, and you will need to scroll to see all the options. Note that changing these options will override the highlighting from the Ensembl features, so you may need to add the Ensembl features again.

From the top right you can also export an image and enter full screen view.