PDB50 at the American Crystallographic Association

The 2021 ACA Transactions Symposium (July 30-31, 2021) was dedicated to celebrating the manifold contributions to fundamental biology, biomedicine, bioenergy, and bioengineering/biotechnology made by PDB Data Depositors and PDB Data Consumers over the past five decades.

Presentations from high profile experimental and computational structural biologists working in the United States, Canada, and South America were augmented by short round table discussions regarding future directions in structural biology and the important role that the Protein Data Bank can play in a rapidly changing landscape.

The Organizing Committee for this symposium included Stephen K. Burley (RCSB PDB), David Rose (University of Waterloo), Natalie Strynadka (University of British Columbia), and Rui Zhao (University of Colorado). Helen M. Berman (RCSB PDB) joined the organizers in chairing the symposium.

This Transactions Symposium was supported by Rigaku, Bruker, and IUCr JournalsPDB50 celebrations and the wwPDB Foundation have been generously supported by Industrial Sponsors

PDB50-related events and resources are highlighted at wwPDB and RCSB PDB.

RCSB PDB Biocurators Gregg Crichlow, Justin Flatt, Brian Hudson, and Yuhe Liang have recorded the details of this landmark meeting.

Session 1 chaired by Stephen K. Burley

Histone H2B Ubiquitination in Transcription Regulation

Cynthia Wolberger

Cynthia Wolberger (Johns Hopkins) began by acknowledging the transformative role the PDB has played in biology and biomedicine over the past 50 years, both in the free sharing of 3D macromolecular structure data and in the development of tools for their analysis and visualization. She then recounted her own research into the central roles post-translational histone modifications have in transcription regulation, presenting cryo-EM structures that reveal how the unique histone methytransferases human Dot1L and yeast COMPASS engage H2B-ubiquitinated nucleosomes, and detailing the mechanistic details that underpin the cross-talk between histone ubiquitination and methylation. She discussed the surprising plasticity of the nucleosome histone core and the implications that has for other histone-modifying enzymes, and ended by highlighting how her research is helping to aid drug discovery in areas such as cancer therapy.

Cryo-FIB Milling Improves MicoED Data and Structures

Mike Martynowycz

Mike Martynowycz (HHMI/UCLA) provided an introduction to micro-electron diffraction (microED) and discussed its utility for the determination of very high-resolution protein structures.  He detailed the inherent advantages of the technique, including its use of tiny granular crystals, its low electron dose, and its ability to resolve amino acid side chains.  He then described the use of cryo-focused-ion-beam (cryo-FIB) milling to trim large crystals down to create thin lamellae suitable for microED, and provided examples of its usefulness in the study of membrane proteins, which typically respond poorly to conventional techniques for preparing microcrystals for microED.

Session 2 chaired by Natalie Strynadka

Macromolecular Machines at Energized Membranes

John Rubinstein

John Rubinstein (Sick Kid’s Hospital, Toronto, Canada) spoke on the ATP synthases and transmembrane proton gradients that create the energized membranes vital for cellular respiration.  He and his group have made use of the recent extraordinary improvements in model resolution accessible using 3DEM and advances in 3DEM hardware and software (for focused refinement, in particular) to illuminate the high-resolution structures and conformational dynamics of large, complex, membrane-associated bioenergetic machines.  He presented the structures of electron transport supercomplexes and ATP synthase from mycobacteria, giving special emphasis to how these data contribute to biomedical outcomes such as the use of the inhibitor Bedaquiline as a treatment for tuberculosis.  He also discussed mechanisms of the activity of these and related enzymes and how 3DEM can be used to understand them in step-by-step detail.

Crystallographic Snapshots of TsrM, a Cobalamin-Dependent S-adenosylmethionine Methylase

Squire J. Booker

Squire J. Booker (Penn State) presented structure/function studies of cobalamin-dependent radical S-adenosylmethionine methylases, which act as “the cell’s universal methylating agent”, catalyzing a number of biologically important reactions.  He focused on TsrM as a model of the superfamily, discussing the importance of the iron-sulfur cluster–coordinated by conserved cysteine residues–which in its reduced form commonly catalyzes the reductive cleavage of SAM to methionine and a 5’-deoxyadenosine 5’-radical that initiates catalysis by abstracting a hydrogen atom from the target substrate.  He presented the first structure of a class B methylase and shared insights into how the enzyme performs three sequential radical-mediated methylations of a single substrate.

Developing Novel Tools to Guide the Discovery of New Cell-permeable, On-target Anti-infective Compounds

Rafael M. Couñago

Rafael M. Couñago (SGC/UNICAMP, Brazil) began by noting how the open nature of the PDB provides immediate access for researchers with limited resources to the structural data associated with cutting edge science.  He then introduced his laboratory–originally begun with a focus on protein kinases–and their work on the development of chemical probes for identifying and studying cell-permeable compounds that have on-target activity in cells, using publicly-available structures in the PDB as guide. He discussed bioluminescence resonance energy transfer (BRET), an inexpensive fluorescence-based strategy that can be used to investigate permeability, binding affinity, and residence time of compounds to their molecular targets in live cells. He presented the compelling example of developing a cellular target engagement assay for the Leishmania parasite, where a chemical probe must cross numerous membrane layers to be effective.

A Global Consortium, Next-generation SARS-COV-2 Antibody Therapeutics and Stabilized Spike

Erica Ollman Saphire

Erica Ollman Saphire (La Jolla Institute for Immunology) discussed the global Coronavirus Immunotherapy Consortium (CoVIC), which brings together academic researchers, non-profit groups, biotechnology companies, and major corporations from around the world to address the pressing need for potent, selective antibody therapeutics to prevent and treat COVID-19. A major accomplishment of the consortium has been the standardized side-by-side comparison of leading monoclonal antibodies for the purpose of identifying the most effective pairings for formulating cocktails to combat spread of the virus and its emerging variants.  Taking lessons from previous collaborative work on Ebola virus, CoVIC has ensured a new framework for research and data sharing in efforts to improve outcomes for COVID-19, with the key to  success being a standardized pipeline that relies on specialized expertise and comprises a series of steps that ensure that the right experiments are performed in a timely manner and that data are carefully aggregated while protecting intellectual property.

Panel Discussion

The panel discussed the possible applications of AlphaFold models and their impact on structural biology. The importance of experimental validation was stressed.

David Rose (ACA president and chair of this Nobel Lecture) welcomed all participants

Nobel Lecture: Innovation by Evolution: Bringing New Chemistry to Life

Frances H. Arnold

Frances H. Arnold (Caltech) discussed protein engineering and the ambition to both improve and diversify protein function beyond that which occurs naturally.  While humanity has been using artificial selection to alter biological systems for thousands of years, the tools provided by modern molecular and structural biology have vastly expanded the potential for generating functional diversity and cultivating novel protein function.  She described the use of “fitness landscapes” to guide directed evolution with the aid of experimental data (such the contents of the PDB) and insights from computation (such as AlphaFold), but noting that many mutations that make a protein fit for new or improved function may be distant from the active, positioned in ways that may not be predictable or explicable.  She concluded by sharing the story of the directed evolution of cytochrome c into a carbon-silicon bond-forming enzyme, a previously unknown enzyme activity.  

The next session was chaired by Rui Zhao

Reflections on Resolution and Revolution––the PDB and me

Wayne A. Hendrickson

Wayne A. Hendrickson (Columbia University) said he began this talk in 1971 at the meeting that established the PDB, describing the state of crystallography at that time and lack of available tools to aid in structure determination. He then focused on the technological and experimental revolutions that have allowed X-ray crystallography to progress to become what it is today, providing the specific example of the use of SAD to solve the structure of crambin.  He then drew a parallel to the “resolution revolution” experienced by 3DEM in recent years, showing structures determined by his group using crystallography and 3DEM throughout his career to highlight how much structural biology has changed in the past half century. He concluded with a discussion of Hsp70 molecular chaperone structures and the insights they provide into intermediate states along the transition pathways of the chaperone cycle.

Structural biology response to biomedical threat

Wladek Minor

Wladek Minor (University of Virginia) spoke on the COVID-19 pandemic and the societal and scientific issues that must be addressed as we learn more about the virus, and about how scientists need to but have so far failed to present a unified message that provides clarity in the face of societal misinformation and skepticism.  To that end, he discussed the role that structural biology has played during the pandemic, emphasizing the rapid pace at which SARS-CoV-2 structures have been added to the PDB and highlighting the need for careful validation to prevent errors being made in haste.  Emphasizing that structure-based drug discovery depends critically upon highly accurate information, he presented a new resource, covid-19.bioreproducibility.org, that provides careful re-refinements of over one hundred SARS-CoV-2 structures and encourages authors to make use of the feedback to update their models.

Helen M. Berman chaired the final session

Protein folding computed from evolutionary information

Chris Sander

Chris Sander (Harvard Medical School) spoke on the application of evolutionary information to the prediction of 3D protein folding.  He traced his history of 3D structural model generation using evolutionary restraints derived from multiple sequence alignments from its early origins to today’s EVfold webserver (evcouplings.org/), and discussed how both the PDB and modern sequencing technologies have made it a viable technique.  He detailed his team’s work to determine 3D models of evolved antibiotic resistance proteins based on constraints derived entirely from genetic experiments and concluded by discussing recent outcomes reported from AlphaFold and providing reassurances that prediction and experiment are and will remain complementary approaches to 3D structure determination.

Structural Relationships between human transcriptional coactivators TFIID and SAGA

Eva Nogales

Eva Nogales (HHMI/UC Berkeley) presented her group’s research on the complexity and modularity of the large coactivator complexes TFIID and SAGA, both challenging systems to study due to the inherent flexibility that is critical to their function. Careful and exhaustive 3DEM studies have revealed the location of the lobes of TFIID and demonstrated that the complex must switch shape to interact with cofactors and bind DNA. 3DEM work on the megadalton SAGA complex, which contains several distinct modules, have yielded powerful insights into how the assembly serves as a regulatory hub in transcription.

From integrative structural biology to cell biology

Andrej Sali

Andrej Sali (RCSB PDB/UCSF) spoke on harnessing integrative modeling approaches to biomolecular network mapping and spatiotemporal modeling of the whole cell. He detailed the development of Bayesian metamodeling as a “divide-and-conquer” strategy for linking and combining heterogenous input models, based on any type of data using any mathematical representation, scale, and level of granularity, to model much larger systems.  He provided the example of glucose-stimulated insulin secretion in pancreatic beta cells as the testbed for how the approach works, demonstrating that a successful model must be spatiotemporal, multiscale, integrative, accurate, and precise; it must reflect uncertainty, rationalize data, predict outcomes, guide experiments, and be iteratively improvable and harmonized. He introduced PDB-Dev, a prototype wwPDB repository for archiving, validating, and analyzing integrative structures, and provided a vision for a future where the scope of structural biology has been expanded with links to integrative models of structure and function.

Panel Discussion

The panel discussed the future of the PDB, both as a hub for integrating and accessing structural and related data in an evolving internet and as a framework for the development of federated resources to archive, maintain, and make available the coming information flood of which AlphaFold is a harbinger.