Exploring protein symmetry at the RCSB Protein Data Bank

Area of Science:

• Structural biology
• Biochemistry
• Bioinformatics

Background:

• The Protein Data Bank (PDB) is a crucial global archive for 3D biomolecular structures.
• Molecular symmetry is a recurring feature in biological macromolecules, observed since early structural studies.
• Approximately 40% of PDB entries display some form of symmetry (global, local, or pseudosymmetry).

Purpose of the Study:

• To highlight the prevalence of symmetry in biological molecules within the PDB archive.
• To introduce the resources and tools provided by the Research Collaboratory for Structural Bioinformatics (RCSB) PDB for exploring biomolecular symmetry.
• To facilitate user exploration of functional biomolecular symmetry.

Main Methods:

• Utilizing the Protein Data Bank (PDB) as the primary data source for structural information.
• Analyzing the PDB archive to quantify the proportion of structures exhibiting symmetry.
• Leveraging RCSB PDB tools for searching, browsing, visualization, and accessing documentation related to biomolecular structures and their symmetries.

Main Results:

• A significant portion (roughly 40%) of archived biomolecular structures exhibit various types of symmetry.
• The RCSB PDB provides comprehensive resources for investigating these symmetries.
• Tools include advanced search/browse functionalities, visualization methods, and educational materials.

Conclusions:

• Symmetry is a common and important feature in biological macromolecules.
• The RCSB PDB actively supports the structural biology community by providing accessible tools to study molecular symmetry.
• Further exploration of biomolecular symmetry can enhance understanding of biological function.