In 1971, the structural biology community established the single worldwide archive for macromolecular structure data–the Protein Data Bank (PDB). From its inception, the PDB has embraced a culture of open access, leading to its widespread use by the research community. PDB data are used by hundreds of data resources and millions of users exploring fundamental biology, energy, and biomedicine. The inaugural PDB50 event, hosted by the wwPDB Foundation and the American Society for Biochemistry and Molecular Biology (ASBMB) was held virtually May 4-5, 2021.
RCSB PDB Biocurators Brian Hudson and Gregg Crichlow have recorded the details of this landmark meeting.
Chaired by Janet Thornton (EMBL-EBI) with introduction from Celia Schiffer (University of Massachusetts Medical School).
Helen M. Berman (Rutgers University and University of Southern California) recounted the origin and history of the PDB from its inception at a 1971 Cold Spring Harbor meeting to the present day, and paid tribute to the people who have made the PDB possible. She detailed the early history of the PDB under Walter Hamilton and Thomas Koetzle at Brookhaven, its eventual move to Rutgers under her own leadership, and the establishment of the wwPDB to ensure a common set of data standards and practices. The importance of the development of community-accepted and -recommended validation standards was noted. She highlighted the idea of the PDB as a living archive, designed and maintained to keep three-dimensional macromolecular structure data public and available to the community and to change and adapt according to community needs and evolving technologies.
Stephen K. Burley (Rutgers and UCSD/SDSC) discussed the influence of the PDB on the process of drug discovery and the massive impact the modern PDB has had on new FDA drug approvals. Between 2010 and approximately 2018, nearly 200 new molecular entities (NMEs) approved by the FDA as drugs and over 70 new cancer drugs have had a basis in thousands of three-dimensional macromolecular structures archived by the PDB representing approximately 100 billion dollars in NIH funding. He then went on to present case studies showing some of the specific impacts PDB data has had on drug development, our understanding of immunology, and antibody engineering for the treatment of cancer.
Zihe Rao (ShanghaiTech University, Tsinghua University), who began studying SARS in 2003, presented his laboratory’s work on the SARS-CoV-2 replication and transcription complex (RTC), including elucidation of the steps involved in its function, from (a) complex formation to (b) helicase-driven RNA elongation (transcription and replication) to (c) the four steps of cap production to (d) interaction with the host cell ribosome. He described the advantages of marshalling joint groups to rapidly solve structures characterizing each of the steps. He also described how their work reveals the molecular basis of inhibition of RTC by remdesivir and the mechanism of proofreading by backtracking.
Alexandre M. J. J. Bonvin (Utrecht University) spoke on the development of docking software and benchmarks using the PDB as a resource. He described the use of HADDOCK (High Ambiguity Driven biomolecular DOCKing) to make use of numerous experimental techniques that may partially characterize a macromolecular structure and its interactions (e.g., ambiguous and/or low-resolution data from NMR titrations, H/D exchange, FRET, cross-linking, residual dipolar couplings, bioinformatics, mutagenesis, etc.), computationally supplemented using docking to create integrative models. He also discussed the validation of integrative models, the development of PDB-Dev, efforts to predict membrane protein interactions, and dynamic energy landscape modeling as the future of structural biology.
Chaired by Thomas Koetzle (Director Emeritus, PDB at Brookhaven National Laboratory)
Eddy Arnold (Rutgers University) spoke on how HIV-1 reverse transcriptase (RT) structures characterizing multiple states of the enzyme have been used to guide the development of anti-AIDS drugs. He discussed his fruitful collaboration with Dr. Paul Janssen, founder of Janssen Pharmaceuticals (now a division of Johnson and Johnson), and about how combining insights from two entirely different approaches to drug discovery led to the development of non-nucleoside reverse transcriptase inhibitors (NNRTIs) that bind distal to the HIV-1 RT active site. He concluded with discussion of structures of the HIV pol protein in the context of the polyprotein.
Hao Wu (Harvard Medical School, Boston Children's Hospital) spoke about inflammasomes and her group’s work on how gasdermin D mediates IL-1 release as part of inflammatory cell death. Gasdermin D binds acidic lipids and undergoes a dramatic conformational change in which multiple subunits form a huge beta barrel that creates pores in cell membranes that selectively pass IL-1 based on charge. Structures of two states (pore, pre-pore) were obtained simultaneously using 3DEM, providing insights into membrane curvature and membrane repair. High-throughput methods have been used to identify inhibitors such as disulfiram (Antabuse) that may be used to treat inflammatory diseases.
Jennifer L. Martin (University of Wollongong) provided a personal retrospective on how her career has intersected and entwined with the PDB as it has grown. She provided her “Top 5 Reasons to Love the Protein Data Bank”: (1) open access data with myriad uses conforming to FAIR principles, (2) a collaborative community with research integrity, (3) the availability (early in the life of the archive) of personalized PDB codes, (4) expert curation, visualization, and analysis of structural data, and (5) the protein structure diversity available in the PDB and the “wonder and awe of Nature” that it engenders. Using HIV-1 reverse transcriptase structures to guide anti-AIDS drug discovery.
Chaired by Joel Sussman (Weizmann Institute of Science; Director Emeritus, PDB at Brookhaven National Laboratory), who shared his view that molecular conformational dynamics is the direction in which structural biology is moving.
Johann Deisenhofer (University of Texas Southwestern Medical Center) reminisced on the early days of the PDB and his uncertainty at the time that an archive of three-dimensional macromolecular structures was necessary. He then went on to detail the various technical and scientific advances (more and better synchrotron facilities, sensitive detectors, crystal freezing, automatic data collection systems, new approaches to the phase problem, powerful cheap computing, new software, DNA sequencing, heterologous protein expression, tailoring of protein domains, labeling techniques, site-specific mutation) that resulted in the eventual explosion in the number of solved structures and disabused both him and other early skeptics of any uncertainty regarding the necessity of the PDB. He then went on to recount the structure determination of the photosynthetic reaction center and its journey to the PDB.
Juli Feigon (University of California, Los Angeles) began with her experiences solving the first DNA quadruplex structure using NMR, then moved on to her investigation of the structural biology of telomerases. Telomerase extends the 3’ ends of linear chromosomes using a transcriptase (TERT) and an integral telomerase RNA (TER) and is a highly regulated determinant of cellular aging that is upregulated in cancer cells. In addition to the TERT/TER core, she discussed the full, dynamic telomerase complex (having additional proteins both transiently and constituently associated with it) and how her group has made use of multiple experimental techniques (MX, NMR, and 3DEM) to unlock its secrets.
Thomas L. Blundell (University of Cambridge) presented a personal history of five decades of structural biology and the PDB, from early work with insulin through HIV-1 protease inhibitor development to recent work on the characterization of large complexes using 3DEM. He recounted his memories of work in the laboratory of Dorothy Hodgkin and of writing the textbook Protein Crystallography with Louise Johnson. He spoke of manipulation of structural selectivity in drug design and his co-founding of Astex Therapeutics to do fragment-based drug design. Finally, he discussed the study of multiprotein systems for DNA repair.
Chaired by Shoshana Wodak (Vrije Universiteit Brussel)
Stephen L. Mayo (California Institute of Technology) spoke on his work in computational protein design. He began with an example of full sequence design, but then moved to an examination of the progression from antibody-drug conjugate (ADC) technology to the development of antibodies possessing a small molecule conjugate incorporated into the paratope. His group has tested this design concept using nanobodies, followed by experimentally guided optimization of the conjugation and of the nanobody.
Wah Chiu (Stanford University) provided his perspectives on improvements in electron microscopy over the last fifty years, beginning with Glaeser’s experiments in electron crystallography in the early 1970’s. He then reviewed the increasing quality and resolution of 3DEM structures over the years–using apoferritin as an example–and discussed Q scores as an evaluation metric. He described the use of 3DEM for RNA structures and statistics for RNA-containing structures by method, in particular for the tetrahymena ribozyme structure. He reviewed the growth of 3DEM depositions in the PDB and EMDB over the years, the initial efforts to develop validation standards, and lastly subcellular component visualization using tomography.
Angela M. Gronenborn (University of Pittsburgh) related her perspectives on NMR structures in the PDB and the use of complementary techniques (e.g., NMR and SAXS) to solve larger problems that neither will solve separately. Sometimes one is forced to solve domain structures due to poorly structured linkers. She discussed the use of different methodologies for determining inter-domain orientations when domains are separated by poorly structured linkers, then described the use of integrative methods to determine the atomic structure of the full HIV-1 capsid.
The seminars were concluded by the presentation of poster prize awards and remarks from the various wwPDB principal investigators, who shared their own “top 5 reasons to love the PDB”.