FOCUS | eDitorial FOCUS | editorial Happy anniversary, PDB! We celebrate the 50th anniversary of the together with our colleagues at Nature Methods with a special collection that showcases key achievements in and views of its future.

n October 1971, the establishment of the PDB was also instrumental in the Structural biologists have traditionally of a central open repository for development of software tools that allow the used a ‘divide-and-conquer’ approach to Imacromolecular structure data, the visualization, validation, analysis and storage address these complex questions, analyzing Protein Data Bank (PDB), was announced of data. In the early days, single proteins or protein domains. This in Nature New Biology (Nat. New Biol. 233, facilitating data access was far from trivial. tactic has in part been necessary due to 223 (1971)). This new repository, which at The process that was created to allow remote technical limitations, but reconstituting the time contained seven structures, was computers to connect and to search data a biological system from its individual the culmination of grassroots efforts led by stored at Brookhaven National Laboratory components in vitro is also an important a cadre of protein crystallographers who was a forerunner to the internet-based pathway toward new knowledge. As Richard were keenly aware of the value of archiving systems that we do not think twice about Feynman aptly put it, “What I cannot create, and sharing X-ray crystallography data, today. As a testament to its success, the I do not understand.” including atomic coordinates, structure PDB now hosts more than 175,000 Despite the success of such reductionist factors and electron density maps. structures. The vast majority have been approaches, molecules do not act in Initially, it was operated by Brookhaven obtained by X-ray crystallography, but the isolation. It is essential to analyze biological National Laboratory and the Cambridge PDB is also the home for atomic models macromolecules in their physiological Crystallographic Data Centre. Since 2003, obtained by NMR spectroscopy (via the context to appreciate their spatial the Worldwide PDB (wwPDB) has been Biological Magnetic Resonance DataBank, relationships and functional interactions. distributed from centers located on three or BMRB) and by 3D electron microscopy Recent technological developments, for continents: the Research Collaboratory of (via the Electron Microscopy Data Bank, example in cryo-electron tomography, Structural Bioinformatics (RCSB) PDB in or EMDB). have made it possible to view molecular the US, the EMBL-EBI’s PDB in Europe As Helen Berman describes in her complexes in their native environment (PDBe) and PDB Japan (PDBj). Together, Comment “Synergies between the Protein and to start understanding the molecular these centers maintain a single archive Data Bank and the community”, such an architecture of tissues and organisms. of macromolecular structure data that is accomplishment would not have been Moreover, integrative or hybrid modelling freely and publicly available to the global possible if the endeavor had not been a has enabled structural models to be built community (Nat. Struct. Mol. Biol. 10, community initiative. It required extensive using a combination of experimental and 980 (2003)). effort, appeals and painstaking consensus computational techniques; these models can PDB data are used by researchers building to bring together the heterogeneous currently be deposited and shared via the worldwide to explore fundamental questions research communities served by the PDB, prototype archive PDB-Dev. about the mechanism and function of with their different interests and needs, to These and other advances are discussed biological macromolecules and how they develop common standards for data in a series of Comments in Nature Methods, can be manipulated to combat disease. sharing and to ensure the success that the introduced in the journal’s Editorial for the As a prime example of the latter, specially PDB now enjoys. May issue, in which researchers from diverse prepared PDB resources provide access to all The PDB has played a central role in areas of structural biology share their views available SARS-CoV-2 PDB structures and shaping how we see the molecular world. on the challenges and opportunities that lay highlight their important structural features Our ability to visualize the diverse shapes ahead. to support structure-based and of proteins and nucleic acids, and thus The fact is, no single technique will allow vaccine development in the fight against the to virtually build cells from molecules us to obtain a mechanistic understanding COVID-19 pandemic. and organisms from cells, helps us to of complete biological systems; only the PDB resources are also used beyond understand life at a fundamental level. integration of multidisciplinary approaches the research community. PDB-101, the Artistic techniques are essential for this and new synergies between cellular and PDB’s education portal, provides teaching visualization, and art can contribute molecular biology will achieve this feat. We materials and introduces students and the substantially as a means of scientific look forward to seeing these developments wider public to the beauty of the molecular discovery, as elaborated on in the Comment come to light, both in our pages and basis of life. “Art as a tool for science” by David Goodsell. elsewhere. ❐ The visionaries who set up the PDB Creating illustrations of concepts and pioneered data-sharing practices at a models can reveal discrepancies and gaps in time when this was still foreign to many our knowledge and inspire new hypotheses Published online: 7 May 2021 other scientific disciplines. The creation and questions. https://doi.org/10.1038/s41594-021-00598-2

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