{"doi":"10.1016/j.jbc.2021.100561","title":"The PDB and the ribosome","abstract":"This essay, which was written to commemorate the 50th anniversary of the Protein Data Bank, opens with some comments about the intentions of the scientists who pressed for its establishment and the nature of services it provides. It includes a brief account of the events that resulted in the determination of the crystal structure of the large ribosomal subunit from Haloarcula marismortui. The magnitude of the challenge the first ribosome crystal structures posed for the PDB is commented upon, and in the description of subsequent developments in the ribosome structure field that follows, it is pointed out that cryo-EM has replaced X-ray crystallography as the method of choice for investigating ribosome structure. This essay, which was written to commemorate the 50th anniversary of the Protein Data Bank, opens with some comments about the intentions of the scientists who pressed for its establishment and the nature of services it provides. It includes a brief account of the events that resulted in the determination of the crystal structure of the large ribosomal subunit from Haloarcula marismortui. The magnitude of the challenge the first ribosome crystal structures posed for the PDB is commented upon, and in the description of subsequent developments in the ribosome structure field that follows, it is pointed out that cryo-EM has replaced X-ray crystallography as the method of choice for investigating ribosome structure. The 50th anniversary of the Protein Data Bank (PDB) is an occasion worth celebrating. It has done everything its founders could possibly have hoped for. At the beginning, it was a tiny operation embedded in the Chemistry Department of Brookhaven National Laboratory. Today it is a large, multi-institutional organization (Rutgers, UCSD, and UCSF) that is part of international consortium called the Worldwide PDB, the members of which are the RSCB (USA), PDBe (Europe), PDBj (Japan), and the Biological Magnetic Resonance Data Bank (BMRB). The PDB would not exist today if a succession of public-spirited scientists had not devoted themselves to it. Walter Hamilton was its first manager, and following his untimely death in 1973, Tom Koetzle took over. Tom was succeeded by Joel Sussman in 1994. In 1999, the PDB was moved from Brookhaven to Rutgers, the home institution of its next director, Helen Berman. Fifteen years later, Helen was succeeded by Stephen Burley. We owe them a lot. Credit is also due to the managers of the agencies that have supported the PDB financially: primarily DOE, NSF, and NIH. At the time of it was founded, the PDB was a very strange duck indeed, and in the early 1970s, no one would have had any reason to be surprised if these agencies had refused to fund it. Happily, their managers understood the importance of the benefits that might be realized if some of the research funds they were responsible for were used to support an enterprise that was, and still is, a public utility. The rest, as they say, is history. As everyone knows, the PDB is a publicly accessible repository of information about the positions of atoms in biological macromolecules, and the essence of what it provides its users are sets of coordinates that specify the locations of most, if not all, of the atoms in particular macromolecules. Even though biochemists routinely use the word “structure” to describe these coordinate sets, it is important to realize that they are not structures. The structure of a macromolecule is the actual arrangement of its constituent atoms in three dimensions, about which our knowledge will always be imperfect to some degree. A coordinate set is an atomic model of a structure that rationalizes the by a particular done to it. The of the word “structure” with coordinate sets was of in the early of the PDB they were the by that had by X-ray It is to that have and it knowledge of a and the structures of its from crystal structures that have The is a of the coordinates and of a large of the atoms in the mac","journal":"Journal of Biological Chemistry","year":2021,"id":201020,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.7333,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":779313,"name":"Peter B. Moore","orcid":"0000-0002-8538-2276","position":0,"is_corresponding":true}],"reference_count":53,"raw_metadata":null,"created_at":"2026-07-18T23:50:52.535403Z","pmid":"33744288","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}