![]() ![]() Figure 1A,B exemplify one aspect of these imperatives: genetic parsimony. Monod succinctly proposed ‘ finiteness, stability, and self-assembly’ as drivers for the evolution of symmetrical assemblies, and since then, the many morphological, energetic, and evolutionary advantages of symmetry have been extensively studied and confirmed. Images adapted from Molecule of the Month and rendered here at a consistent scale. ( E) Insulin is stored in pancreatic cells as micro-crystals of hexamers of heterodimers stabilized by zinc ions (left, red and tan denoting insulin α and β chains, respectively cyan circle: zinc ion) (PDB id 4ins ), but is active as a single heterodimer when bound to its receptor (receptor in blue at right) (PDB id 6pxv ). ![]() ( D) Aspartate carbamoyltransferase is a symmetrical allosteric enzyme that transitions between inactive (left) (PDB id 5at1 ) and active (right) (PDB id 1d09 ) conformations. ( C) ATP synthase has a chemical F1 motor with three-fold symmetry (red) and a membrane-embedded F0 motor with ten-fold symmetry (turquoise) connected by an asymmetric axle (dark blue), which are then arranged in pairs with 2-fold symmetry (PDB id 6b8h ). ( B) Virus capsids use icosahedral quasisymmetry to build large structures from multiple identical subunits packed into slightly different local environments (PDB id 2tbv ). ( A) Ribosomes are among the largest asymmetric assemblies found in living organisms (based on PDB ids 4v4q, 1rqu ). After a short introduction, we will devote the bulk of this article to describing tools at the Research Collaboratory for Structural Biology (RCSB) Protein Data Bank (PDB) for finding, visualizing, analyzing, and exploring aspects of symmetry within the PDB archive of more than 190 000 experimentally determined, atomic-level 3D structures of biological macromolecules. Principles of biomolecular symmetry, its functional and evolutionary consequences, and the many structural and functional exceptions to symmetry have been extensively covered elsewhere, and are beyond the scope of this brief review. In 1956, for example, Crick and Watson correctly predicted that cubic symmetries would be uniquely suited to building the hollow shells of spherical viruses. Such arrangements were predicted from first principles before any atomic-level three-dimensional (3D) structures of biomolecules were determined. In most cases, these assemblies are composed of multiple identical subunits arranged symmetrically. Figure 1 exemplifies the scope of what is already known about symmetric assemblies. When browsing the PDB archive, we find myriad examples of individual proteins arranged in the shape of rings, containers, channels, filaments, sheets, and complex molecular machines, all tailored to fulfill particular functional roles. Symmetry of biological macromolecules is a classic example of the structural biology tenet: function follows form. These tools include multiple modalities for searching and browsing the archive, turnkey methods for biomolecular visualization, documentation, and outreach materials for exploring functional biomolecular symmetry. The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (founding member of the Worldwide Protein Data Bank partnership that jointly manages, curates, and disseminates the archive) provides a variety of tools to assist users interested in exploring the symmetry of biological macromolecules. ![]() Roughly 40% of the structures in the archive exhibit some type of symmetry, including formal global symmetry, local symmetry, or pseudosymmetry. The Protein Data Bank (PDB) archive is the central global archive of three-dimensional (3D), atomic-level structures of biomolecules, providing open access to the results of structural biology research with no limitations on usage. The symmetry of biological molecules has fascinated structural biologists ever since the structure of hemoglobin was determined. ![]()
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