Work

Frozen in Motion: FAIR and Sustainable Data Management in Cryo-EM at the Worldwide Protein Data Bank

Year: 2024

Type: article

Abstract: The Protein Data Bank (PDB) was established in 1971 as the first open-access digital data resource in biology, initially comprising just seven X-ray crystal structures of proteins. Today, it houses more than 215,000 experimentally-determined three-dimensional (3D) structures of biological macromolecules that are freely used by many millions of PDB data consumers worldwide [1-3]. This wealth of information serves as a cornerstone for basic and applied research and education endeavors across fundamental biology, biomedicine, biotechnology, bioengineering, and energy sciences [4]. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org), which currently consists of five full members (RCSB PDB, PDBe, PDBj, BMRB, and EMDB) and one associate member (PDBc). Today, wwPDB partners jointly manage three Core Archives, including PDB (archiving atomic coordinates and crystallography data), EMDB (archiving 3DEM density maps), and BMRB (archiving NMR data), all the while adhering to the FAIR (Findability, Accessibility, Interoperability, Reusability and FACT (Fairness, Accuracy, Confidentiality, Transparency) principles emblematic of responsible data stewardship. Cryo-electron microscopy continues to undergo rapid transformation as we transition from the decade of the "Resolution Revolution" into a new era characterized by the convergence of artificial intelligence, machine learning, and automation. These transformative changes have been propelled by advancements in microscopy, detectors, and image processing algorithms, resulting in improved speed and precision in structural analysis [5]. Consequently, the number of new 3D electron microscopy (3DEM) structures released annually from the PDB is poised to surpass those from X-ray crystallography, marking a significant shift in structural biology methodologies. Consequently, the number of structures released annually to the Protein Data Bank archive from 3D electron microscopy (3DEM) is poised to surpass those from X-ray crystallography, marking a significant shift in structural biology methodologies. Notably, some of these structures, such as PDB ID 6z6u and 7a4m, have achieved true atomic resolution, enabling determination of the precise localization of individual atoms within the 3DEM density map. Advances in cryo-electron microscopy owe much to the standardization of 3DEM workflows, data formats, and validation protocols, alongside responsible data stewardship guided by FAIR and FACT. These frameworks have played critical roles in fostering collaboration, ensuring data integrity, and maximizing the impact of 3DEM research [6-9]. This presentation will explain how the infrastructure underpinning archiving of 3DEM data works, covering development of the global unified OneDep system that supports complete deposition, rigorous validation, expert biocuration annotation, and timely release of 3DEM structures to the public [10]. The discussion will explore how automation can enhance data harvesting and improve data depositor and wwPDB biocurator efficiency, which is essential in the face of year-on-year increase in the number of new 3DEM structures stored in PDB.

Source: Microscopy and Microanalysis

DOI: 10.1093/mam/ozae044.182