Secondary structure variance on PDBe-KB aggregated views of proteins

Secondary structure variance image

The display of protein secondary structure data along a 1D sequence is important for showing structural context for protein sequences. However, this has routinely only shown discrete secondary structure for an individual protein structure, rather than across a population of structures

PDBe team members worked with Adam Midlik from the Svobodová group at CEITEC, to implement a process for visualisation of secondary structure variation for a particular UniProt protein accession across all PDB entries. Our process calculates the relative frequency of alpha-helices, beta-strands and loop regions for each observed amino acid. This information can be accessed on the structure page of the PDBe-KB aggregated views of proteins, displayed on the ‘secondary structure variation’ track in the ProtVista sequence viewer.

The secondary structure variation track displays separate rows for each of helices (pink), strands (yellow) and loop regions (grey). This track can be expanded by clicking on the blue label on the left hand side, displaying the three secondary structure rows as separate tracks. The intensity of the colour at each position is relative to the frequency of that secondary structure for that specific position in the protein sequence. This can therefore highlight regions that always exhibit the same secondary structure, and other regions that may have different secondary structure in other structures.

The identification of variation in secondary structure across different structures can give insights into important features of the protein. This can include highlighting regions of structural plasticity or that may form different conformations under different conditions or with different molecules bound. Some classes of proteins that commonly include regions of secondary structure variance include transcription factors and amyloid.

 

ProtVista on the Structures page for Retinoic acid receptor alpha (UniProt accession P10276), with the secondary structure variation track expanded. The region around residues Arg394 - Lys399 adopts different secondary structure across PDB entries, with the highlighted amino acids Thr397 showing a ratio of 75% helical, 16.7% beta strands and 8.3% loops.
ProtVista on the Structures page for Retinoic acid receptor alpha (UniProt accession P10276), with the secondary structure variation track expanded. The region around residues Arg394 - Lys399 adopts different secondary structure across PDB entries, with the highlighted amino acids Thr397 showing a ratio of 75% helical, 16.7% beta strands and 8.3% loops.

 

In the example above, for the Human protein Retinoic acid receptor alpha, the region around residues Arg394 - Lys399 varies in the secondary structure formed across the structures in the archive. This region of the structure undergoes a conformational change upon binding of the coactivator forming a helical structure, however there are some structures in the archive of the corepressor-bound state which instead exhibit beta strand properties at this region. This conformational change and its biological importance is described more fully by le Maire et al. at doi.org/10.1038/nsmb.1855.

To access these pages, visit pdbekb.org/protein and navigate to your preferred UniProt accession, or use the search at pdbe.org and select the UniProt accessions from the search results. For more information on this new feature visit the PDBe-KB manual for secondary structure variance.

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