Protein Symmetry Browser

Browse for structures by global and local symmetry and pseudosymmetry.

This browser gives access to advanced protein symmetry features.

Protein Symmetry

Protein symmetry refers to point group or helical symmetry of identical subunits (>= 95% sequence identity over 90% of the length of two proteins). While a single protein chain with L-amino acids cannot be symmetric (point group C1), protein complexes with quaternary structure can have rotational and helical symmetry.

Rotational and helical symmetries observed in protein quaternary structure.

Complexes are considered symmetric if identical subunits superpose with their symmetry related copies within <= 7 Å Cα RMSD. Protein subunits are considered identical if their pairwise sequence identity is >= 95% over 90% of the length of both sequences, to account for minor sequence variations such as point mutations and truncated or disordered N- and C-terminal segments. Nucleic acid chains, ligands, and protein chains with less than 20 residues are excluded, unless the majority of chains are shorter than a 5-residue cut-off. Split entries (entries divided between multiple coordinate files due to the limitations of the PDB file format) are currently excluded from the protein stoichiometry and protein symmetry features. The symmetry information is calculated for the first biological assembly, if available. Otherwise, it is determined from the PDB entry itself.

Protein Pseudosymmetry

Pseudosymmetry refers to symmetry of homologous protein subunits. Protein complexes with pseudostoichiometry may have a higher structural symmetry than the symmetry calculated based on sequence identity. If we consider hemoglobin again, at a 95% sequence identity threshold the alpha and beta subunits are considered different, which correspond to an A2B2 stoichiometry and a C2 point group. At the structural similarity level, all four chains are considered homologous (~45% sequence identity) with an A4 pseudostoichiometry and D2 pseudosymmetry.

Hemoglobin with 4 homologous subunits (Stoichiometry A4) has D2 pseudosymmetry. In addition to the C2 symmetry (red axis), there are two perpendicular C2 axes (blue).

Global Symmetry

Global symmetry refers to the symmetry of the entire complex. Protein complexes may be symmetric, pseudosymmetric, or asymmetric.

Examples of global protein symmetry

Local Symmetry

Asymmetric protein complexes may have local symmetry. Similar to global symmetry, we distinguish local symmetry of identical subunits and local pseudosymmetry of homologous subunits.

Examples of local protein symmetry

Examples

  1. Type a point group symbol (e.g., C2, C5, D2, T, O, I) or H for helical into the Protein Symmetry Browser text box and choose a symmetry from the autosuggestions. For example, type C5 into the text box and click on one of the autosuggested C5 links. The browser will expand and highlight all matches of C5 in the protein symmetry browser.
  2. Expand the nodes of the protein symmetry browser by clicking on the triangle next to a node. For example, expand 'Global symmetry', then 'Symmetric', then 'Dihedral', and finally click on the D4 link to retrieve all protein complexes with D4 symmetry.