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Cited by 48Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and FunctionProtein Structure and Dynamics

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Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold

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Castells-Graells, Roger, Meador, Kyle, Arbing, Mark A., Sawaya, Michael R., Gee, Morgan, Cascio, Duilio, Gleave, Emma, Debreczeni, Judit É., Breed, Jason, Leopold, Karoline, Patel, Ankoor, Jahagirdar, Dushyant, Lyons, Bronwyn, Subramaniam, Sriram, Phillips, Chris, Yeates, Todd O.·2023·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.2305494120PMC PMC10500258

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Abstract

Cryoelectron microscopy (Cryo-EM) has enabled structural determination of proteins larger than about 50 kDa, including many intractable by any other method, but it has largely failed for smaller proteins. Here, we obtain structures of small proteins by binding them to a rigid molecular scaffold based on a designed protein cage, revealing atomic details at resolutions reaching 2.9 Å. We apply this system to the key cancer signaling protein KRAS (19 kDa in size), obtaining four structures of oncogenic mutational variants by cryo-EM. Importantly, a structure for the key G12C mutant bound to an inhibitor drug (AMG510) reveals significant conformational differences compared to prior data in the crystalline state. The findings highlight the promise of cryo-EM scaffolds for advancing the design of drug molecules against small therapeutic protein targets in cancer and other human diseases.

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Metadata

Authors
Castells-Graells, R., Meador, K., Arbing, M. A., Sawaya, M. R., Gee, M., Cascio, D., Gleave, E., Debreczeni, J. É., Breed, J., Leopold, K., Patel, A., Jahagirdar, D., Lyons, B., Subramaniam, S., Phillips, C., & Yeates, T. O.
Affiliations
  • Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095
  • University of California, Los Angeles (US)
  • AstraZeneca (United Kingdom) (GB)
  • Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, United Kingdom
  • Gandeeva Therapeutics, Inc., Burnaby, British Columbia V5C 6N5, Canada
  • University of British Columbia (CA)
Corresponding author
Yeates, Todd O.
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2023-09-05
Volume
120
Issue
37
Pages
e2305494120-e2305494120
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.2305494120
PMC
PMC10500258
OpenAlex
W4386453144
Cited by
48
References
9
Citations by year
2026: 10 · 2025: 20 · 2024: 14 · 2023: 3
FWCI
4.16
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders
  • HHS | NIH | National Institute of General Medical Sciences (R01GM129854)
  • DOE | Office of Science (DE-FC02-02ER63421)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
protein cages, KRAS, sotorasib, conformational differences, drug target structure
MeSH terms
Diagnostic Imaging, Humans, Cryoelectron Microscopy

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