Browse for structures by global and local symmetry and pseudosymmetry.
This browser gives access to advanced protein symmetry features.
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.
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 refers to the symmetry of the entire complex.
Protein complexes may be symmetric, pseudosymmetric, or asymmetric.
Examples of global protein 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
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.