In an effort to improve the understanding of the structure and function of macromolecular assemblies, a new feature has been introduced to annotate and display symmetry in these structures. This new process, powered by Ananas, provides global symmetry data for each new assembly on a weekly basis. This underlying data is used to populate the symmetry API endpoint, which is utilised by the Mol* viewer to display symmetry-related information.
Ananas, created by the Nano-D team team at Inria/CNRS Grenoble (), works by finding the positions and orientations of the symmetry axes in all types of symmetrical protein assemblies. It deals with five symmetry groups: cyclic, dihedral, tetrahedral, octahedral, and icosahedral. Ananas can also assess the quality of symmetry in the assembly and can detect symmetries in incomplete cyclic assemblies. The method is fast and applicable to assemblies with multiple chains in the asymmetric subunits or those with pseudo-symmetry.
PDBe users can view these new assembly symmetry annotations directly in the Mol* viewer on the PDBe website. This feature is accessible via the “Annotations� section in the right-hand pane of the Mol* viewer. Clicking the eye icon next to “Assembly Symmetry� will retrieve assembly symmetry data from our API and generate the visualisation of the assembly symmetry annotations directly on the structure.
The symmetry visualisation works for any non-trivial symmetry and includes visualisation of symmetry axes and a cage matching the point symmetry group. Please note that the symmetry information is only available for assemblies, therefore the “Assembly Symmetry� row is only shown when “Type� in the “Structure� section is set to “Assembly�. You can also use the PDBe API to access the underlying data that supports this visualisation using the PDBe aggregated API symmetry endpoint.
The generation of the symmetry type and the symmetry axes for each assembly using this new process can give users additional insight into structures in the PDB. For example, PDB entry 4u7n is an inactive histidine kinase () dimer that consists of two copies of the protein arranged in C2 symmetry. However, there are other instances of this assembly in the PDB archive (e.g. PDB entries 4u7o and 4zki) which appear to lack this C2 symmetry. The individual domains of histidine kinases have been shown to adopt both symmetric and asymmetric conformations in different catalytic states, which might explain the differences in the symmetry groups of these structures.
This new feature will undoubtedly enhance the understanding and study of macromolecular assemblies and indicate how differences in symmetry could affect macromolecular function.
For more information about this new process, view the publication at .
