Education Corner

Structural biology is essential for providing an understanding of the molecular machinery in infectious organisms, a key step for developing new therapeutics and vaccines. For nearly two decades, the National Institute of Allergy and Infectious Diseases (NIAID) Centers for Research in Structural Biology of Infectious Diseases (CRSTAL-ID) have served as a structural biology resource for the infectious disease research community. Investigators at the two centers, the Seattle Structural Genomics Center for Infectious Disease (SSGCID) and the Center for Structural Biology of Infectious Diseases (CSBID), determine the three-dimensional structures of proteins and other biological macromolecules central to pathogen biology and host-pathogen interactions.

Beyond solving structures, the centers make their expertise, data, and research materials freely available to the broader scientific community. This collaborative model has helped to accelerate discoveries across various areas of infectious disease research, enabling many projects that would have been beyond the reach of individual laboratories. In this RCSB Education Corner, we highlight some of the CRSTAL-ID research successes that demonstrate both the breadth of science made possible by this model and the lasting impact the centers have made on structural biology and infectious disease research.

A partial mandate of the centers is to serve NIAID as an immediate response unit in the event of a sudden infectious disease emergence. In the past, the centers responded to the emergence of Zika, Ebola, and antimicrobial resistant (AMR) pathogens. This mandate was particularly important in early 2020 when structural biologists started tackling surface and essential protein structures of the virus then known as 2019-nCoV. As the SARS-CoV-2 pandemic grew over the next few months, NIAID asked the CRSTAL-ID centers to use their expertise in understanding this new version of the SARS coronavirus. Both the CSBID and SSGCID had experienced structural biologists of viral proteins who had previously determined protein structures from the prior SARS-CoV (2002) and subsequent MERS-CoV (2012) outbreaks. Structural biology provided the atomic-level models of SARS-CoV-2 proteins needed to enable the rapid design of both vaccines and antiviral therapies. By February 2020, David Veesler and his colleagues published high-resolution CryoEM structures of the spike trimer in open and closed conformations and bound with monoclonal antibodies. At the same time, the CSBID undertook a broad spectrum approach across the SARS-CoV-2 genome ultimately determining structures of 10/16 non-structural proteins and 3 structural proteins while initiating drug discovery efforts on the proteases, helicase, and methyltransferases. Altogether, the centers determined 179 structures for SARS-CoV-2 (Fig. 1), out of a total of 4177 (excluding large scale fragment screens), or 4.3% of all structures. Moreover, during that first year, the two CRSTAL-ID centers solved 17% of all SARS-CoV-2 structures, encompassing multiple proteins across each of the newly breaking strains, in swift response to the pandemic.

The groundwork to be capable of tackling novel proteins in crisis times was laid by the NIAID in 2007, with a mandate to apply high-throughput X-ray crystallography, NMR, and eventually CryoEM, to determine the atomic structures of proteins from NIAID category A-C priority pathogens, specifically including organisms linked to biodefense, emerging, and re-emerging infectious diseases. The two centers divide the organisms to avoid duplicating effort, and large bioinformatic screens of known or potential drug targets, essential gene products, virulence factors, proteins involved in host-pathogen interaction and viral antigens are mapped for the NIAID priority pathogens. Cloning, expression, purification, crystallization and structure determination pipelines are established to take on hundreds of protein samples at a time.

A major effort for the CSBID addresses the emerging problem of AMR pathogens, including bacterial enzymes exchanged on mobile elements that confer resistance, such as beta-lactamases (Fig. 2), methyltransferases, and acetyltransferases. Further, the center addresses essential enzymes of high priority AMR pathogens that could function as future targets for structure-guided drug design including membrane proteins essential for cell wall biosynthesis and structures of proteins from Clostridioides difficile, ultimately solving more than 10% of all structures in the PDB for this organism. The C. difficile effort was more successful in recent years primarily driven by advances in synthetic DNA technologies that enabled soluble expression of recombinant proteins optimized with E. coli codon usage. Implementation of synthetic DNA as the primary cloning strategy of the center since 2022 has advanced research into other organisms with suboptimal %GC DNA content including new initiatives in tick-borne bacteria such as Rickettsia and Borrelia spp. as well as increasing efforts for viral proteins.

One of the many bacterial pathogens assessed by the SSGCID is Mycobacterium tuberculosis, a high-priority pathogen particularly due to rapidly evolving multidrug resistance around the globe. Mtb proteins, however, often fail at various early stages of the pipeline as they are insoluble or toxic in high-throughput E. coli expression. One lesson learned along the way is that small sequence changes can make the difference in a protein being soluble or crystallizable. The high-throughput rescue of intractable Mtb proteins was therefore to take intra-genus homologous proteins in other nontuberculous Mycobacterium (NTM) species (such as avium, leprae, smegmatis,  thermoresistibile), use the same high-throughput approach across all species and proceed with whichever version of the protein behaved best through crystallization and structure determination. Of 179 potential TB drug targets selected for X-ray structure determination, only 16 (9%) yielded a crystal structure. Adding homologs from NTM species allowed an additional 52 (29%) otherwise intractable targets to be solved (Fig. 3). Other high-throughput efforts have resulted in the SSGCID depositing the only structures for a priority pathogen (such as Ehrlichia and Balamuthia, or 90% for Coccidioides). Over the last 19 years, depositing roughly 200 high-resolution structures annually to the PDB has greatly enriched public structural knowledge and directly supported the foundation for protein modeling algorithms to evolve rapidly these past five years.

Both CRSTAL-ID centers built substantial bioinformatics resources. In addition to initial proteome screens for pathogen targets, we are expanding our capabilities to include protein design for target stabilization, inhibition, and complex disruption. Our structural bioinformatics pipeline has matured alongside the field, progressing from early RoseTTAFold versions to current AI-driven modeling technologies. The CSBID has established pipelines for structure-based modeling with applications including 3-D mapping of natural mutations in viral proteins and prediction of structure of bacterial porins and function of bacterial toxins. These data are provided to the public to allow biologists to advance their research. The SSGCID uses a large language model in literature mining to improve protein expression protocols.

Both the breadth and the depth of the centers’ efforts allow collaborative work and shared expertise to flourish so that more complex projects have been tackled in recent years. The CSBID has built specialized capabilities for CryoEM to determine complex structures of importance. The structures of whole viruses such as Dengue, Zika, and Enterovirus D68 (Fig. 4) have been solved at high resolution providing a valuable approach for determining antibody recognition on viral surface proteins and ligand binding that can prevent capsid assembly. Similar technologies including viral-like particles and hybrid viruses have facilitated examination of receptor and antibody interactions at viral surfaces, including those of BSL3 restricted pathogens. The CSBID also established a pipeline to determine structures of challenging outer membrane proteins revealing these frequently show distinct structures compared to those from AI modeling prediction algorithms.

The SSGCID tackled a promising protein target, calcineurin, across major human fungal pathogens responsible for over 1.6 million annual cases of invasive fungal infections worldwide, with mortality rates of up to 95%. Developing antifungals is challenging because fungi are eukaryotes and require selective targeting to prevent harming the human host. Crystal structures of fungal complexes of calcineurin with its partner inhibitors (Fig. 5), NMR-based inhibitor binding studies, site-directed mutagenesis of the complex, and molecular dynamic simulations revealed that a key residue, which is not conserved in the mammalian homolog, is essential for binding and inhibiting fungal calcineurin. These results enabled the rational design and development of a less immunosuppressive analog with broad-spectrum in vitro antifungal activity and efficacy in a Collaboration between the two centers thrives as well. The CSBID and SSGCID can divide and conquer; for example, each tackling half of the promising Mycobacterial aminoacyl-tRNA synthetase drug targets or use each center’s strengths to examine protein complexes both structurally and biophysically using protein design, NMR, X-ray crystallography and CryoEM.

The CRSTAL-ID centers have demonstrated that sustained, coordinated investment in structural biology yields excellent returns. Their community-based model, rather than an individual investigator-initiated research, allows the centers to partner with hundreds of research groups providing critical structural biology expertise and resources. This collaborative engine has given many scientists the critical jump-start or final push needed to move their work forward. The capabilities and infrastructure built in CRSTAL-ID are an invaluable resource to the infectious disease research community, especially as new infectious threats continue to emerge. From accelerating a pandemic response within weeks of the pathogen's emergence, to enabling rational design of next-generation antifungals, the SSGCID and CSBID have generated a broad and lasting scientific impact to the infectious disease and structural biology communities.

This project has been funded with federal funds from the National Institute of Allergy and Infectious Diseases (NIAID), NIH, Department of Health and Human Services, under Contract Nos. 75N93022C00035 and 75N93022C00036.

Further Reading

1. Anderson, WF. Structural genomics and drug discovery for infectious diseases. Infect Disord Drug Targets 2009;9: 507–517. https://doi.org/10.2174/187152609789105713
2. Baugh, L, Phan, I, Begley, DW, Clifton, MC, Armour, B, Dranow, DM, Taylor, BM, Muruthi, MM, Abendroth, J, Fairman, JW, Fox, D, 3rd, Dieterich, SH, Staker, BL, Gardberg, AS, Choi, R, Hewitt, SN, Napuli, AJ, Myers, J, Barrett, LK, Zhang, Y, Ferrell, M, Mundt, E, Thompkins, K, Tran, N, Lyons-Abbott, S, Abramov, A, Sekar, A, Serbzhinskiy, D, Lorimer, D, Buchko, GW, Stacy, R, Stewart, LJ, Edwards, TE, Van Voorhis, WC and Myler, PJ. Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) 2015;95: 142–148. https://doi.org/10.1016/j.tube.2014.12.003
3. Dey, S, Gireesan, S, Solovou, T, Inniss, NL and Satchell, KJF. High-Throughput Pipeline for Protein Expression and Solubility Profiling Using Synthetically Generated Plasmids. Curr Protoc 2025;5: e70188. https://doi.org/10.1002/cpz1.70188
4. Dowd, KA, Sirohi, D, Speer, SD, VanBlargan, LA, Chen, RE, Mukherjee, S, Whitener, BM, Govero, J, Aleshnick, M, Larman, B, Sukupolvi-Petty, S, Sevvana, M, Miller, AS, Klose, T, Zheng, A, Koenig, S, Kielian, M, Kuhn, RJ, Diamond, MS and Pierson, TC. prM-reactive antibodies reveal a role for partially mature virions in dengue virus pathogenesis. Proc Natl Acad Sci U S A 2023;120: e2218899120.
5. Hodge, EA, Archer, J, Anderson, JS, Warner, NL, Tremblay, J, Klose, T, Park, S, Hinkley, T, Khandhar, AP, Kuhn, R, Shoemaker, CB and Erasmus, JH. An RNA-to-RNA pipeline for rapid antiviral antibody development. Mol Ther 2026;34: 4136–4152. https://doi.org/10.1016/j.ymthe.2026.04.021
6. Hoy, MJ, Park, E, Lee, H, Lim, WY, Cole, DC, DeBouver, ND, Bobay, BG, Pierce, PG, Fox, D, 3rd, Ciofani, M, Juvvadi, PR, Steinbach, W, Hong, J and Heitman, J. Structure-Guided Synthesis of FK506 and FK520 Analogs with Increased Selectivity Exhibit In Vivo Therapeutic Efficacy against Cryptococcus. mBio 2022;13: e0104922. https://doi.org/10.1128/mbio.01049-22
7. Joachimiak, A. Introduction. Protein Science 2020;29: 623–628. https://doi.org/10.1002/pro.3838
8. Myler, PJ, Stacy, R, Stewart, L, Staker, BL, Van Voorhis, WC, Varani, G and Buchko, GW. The Seattle Structural Genomics Center for Infectious Disease (SSGCID). Infect Disord Drug Targets 2009;9: 493–506. https://doi.org/10.2174/187152609789105687
9. Rosas-Lemus, M, Dey, S, Minasov, G, Tan, K, Anderson, SM, Brunzelle, J, Nocadello, S, Shabalin, I, Filippova, E, Halavaty, A, Kim, Y, Maltseva, N, Osipiuk, J, Minor, W, Joachimiak, A, Savchenko, A, Anderson, WF, Satchell, KJF and Center for Structural Biology of Infectious Diseases Team Members. A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile. Microbiol Resour Announc 2023;12: e0050723. https://doi.org/10.1128/MRA.00507-23

Author info: 

1. Sandhya Subramanian, Center for Global Infectious Disease Research, Seattle Structural Genomics Center for Infectious Disease, Seattle Children's Research Institute, Seattle WA. Sandhya.Subramanian@seattlechildrens.org
2. Karla J. F. Satchell, PhD, Northwestern University Feinberg School of Medicine, Center for Structural Biology of Infectious Diseases, Department of Microbiology-Immunology, Chicago IL. k-satchell@northwestern.edu
3. Alfa Herrera, PhD, Northwestern University Feinberg School of Medicine, Center for Structural Biology of Infectious Diseases, Department of Microbiology-Immunology, Chicago IL. alfa.herrera@northwestern.edu 
4. Krystle J. McLaughlin, PhD, Chemistry Department, Vassar College, Poughkeepsie NY. kmclaughlin@vassar.edu