Protein Symmetry View

Introduction

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. Protein chains with less than 20 residues are excluded, unless at least half of the chains are shorter than 20 residues. Nucleic acids and carbohydrate chains, as well as ligands are excluded. 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.

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



Visualization

Visualizing Protein Symmetry in Jmol

Protein symmetry can be viewed in 3D using Jmol (select the "3D View" link or "3D View" tab on an entry's Structure Summary page). Protein symmetry is calculated for all entries containing at least one protein chain, including asymmetric units and all biological assemblies (except for entries split among several PDB files due to their size).

To facilitate the exploration of symmetry, several options are available:

Default Orientation

View 3EAM

Protein complexes are aligned along the highest-order symmetry axis, helix axis, or along the principal axes on inertia for asymmetric cases. Several default orientations of the structure can be toggled using the < and > buttons. The default orientations are canonical views: sides and back, and along unique symmetry axes.

View PDB ID 3EAM in Jmol

Symmetry polyhedra and axes

View 1AEW

A polyhedron and symmetry axes can be displayed to facilitate symmetry analysis of symmetry. A complex is enclosed in a polyhedron that matches its symmetry. All symmetry axes and their icons representing the fold (ellipsis for 2-fold, triangle for 3-fold axis, or in general a polygon for n-fold axis) can be displayed.

For helical symmetry, a helix axis is displayed and for asymmetric cases, the 3 axes of inertia are displayed. Polyhedron and Axes can be toggled on/off using the check boxes in the right panel.

View PDB ID 1AEW in Jmol

Color by Symmetry

Two examples of structures colored by symmetry are shown below.

Example 1

For Cn symmetry (see example on left), the color scheme start at the 12 o'clock position, and the color gradient (light to dark) increases in a clockwise direction. The polyhedron, a pentagonal prism is displayed in a color complementary to the symmetry color scheme. The principal rotation axis is rendered in red with a pentagon representing the 5-fold rotation.

View PDB ID 3EAM in Jmol


Example 2

In all cubic systems (T, O, I), different layers of the subunit are colored along a gradient (light to dark) from the plus and minus z-axis towards the origin (see example on left). The 4-fold axes are rendered in red, the 3-fold axes in green, and the 2-fold axes in blue. Using the toggle option underneath the Jmol applet, 3 views along these 3 different axes are available.

View PDB ID 1SHS in Jmol


Example 3

For helical symmetry (H), subunits are colored using a spectual gradient along the y-axis.

View PDB ID 1IFD in Jmol


Symmetry Color Schemes

Symmetry Color Scheme Example Image Polyhedron Axes
Cyclic C1
(no symmetry)
grays PDB: 4AJY
Stoichiometry: ABC
Point Group: C1
PDB ID: 4AJY cyclic symmetry C1 rectangular
prism gray
3 axes of inertia
in gray
Cyclic Cn
yellow-green-blue
radial gradient
clockwise
around
symmetry axis
PDB: 4ACV
Stoichiometry: A6
Point group: C6
PDB ID: 4ACV cyclic symmetry Cn hexagonal
prism orange
6-fold red
Dihedral Dn
yellow-orange-
red gradient
along z-axis
towards origin
PDB: 1YA7
Stoichiometry:A14B14C14
Point group: D7
PDB ID: 1YA7 dihedral symmetry Dn heptagonal
prism blue
7-fold red
2-fold blue
Tetrahedral T
green gradient
(light - dark)
along z-axis
towards origin
PDB: 1MOG
Stoichiometry: A12
Point group: T
PDB ID: 1MOG tetrahedral symmetry T tetrahedron
purple
3-fold green
2-fold blue
Octahedral O
blue gradient
(light - dark)
along z-axis
towards origin
PDB: 1SHS
Stoichiometry:A24
Point group O
PDB ID: 1SHS octahedral symmetry O octahedron
orange
4-fold red
3-fold green
2-fold blue
Icosahedral I
blue-purple
gradient along
z-axis towards
origin
PDB: 4FTS
Stoichiometry:A180
PDB ID: 4FTS icosahedral symmetry I icosahedron
green
5-fold red
3-fold green
2-fold blue
Helical H
spectral gradient
along y-axis
PDB: 1IFD
Stoichiometry: A55
PDB ID: 1IFD helical symmetry H not
implemented
helix axis red