Abstract
RAF activation is essential for MAPK signaling and is mediated by RAS binding and the dephosphorylation of a conserved phosphoserine by the SHOC2–RAS–PP1C complex. MRAS forms a high-affinity SHOC2–MRAS–PP1C (SMP) complex, while canonical RAS isoforms (KRAS, HRAS, NRAS) form analogous but lower-affinity assemblies. Yet, cancers driven by oncogenic KRAS, HRAS, or NRAS remain strongly SHOC2-dependent, suggesting that these weaker complexes contribute to tumorigenesis. To elucidate how canonical RAS proteins form lower-affinity ternary complexes, the cryo-EM structure of the SHOC2–KRAS–PP1C (SKP) complex stabilized by Noonan syndrome mutations is described. The SKP architecture is similar to the SMP complex but forms fewer contacts and buries less surface area due to the absence of MRAS-specific structural features in KRAS that enhance complex stability. RAS inhibitors MRTX1133 and RMC-6236 alter Switch-I/II conformations, thereby blocking SKP assembly more effectively than they disrupt preformed complexes. These RAS inhibitors do not affect SMP formation because they do not bind MRAS. Since MRAS is upregulated in resistance to KRAS inhibition, we characterize a MRAS mutant capable of binding MRTX1133. This MRAS mutant can form an SMP complex, but MRTX1133 blocks its assembly, demonstrating the feasibility of dual SKP and SMP targeting. Overall, our findings define isoform-specific differences in SHOC2–RAS–PP1C complex formation and support a strategy to prevent both SKP and SMP assemblies to overcome resistance in RAS-driven cancers.
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Data availability
The atomic coordinates and structure factors have been deposited in the Protein Data Bank and can be accessed using accession numbers 9O65, EMD-70159 (stabilized SKP complex), 9O0N (KRAS(1-169)GDP with MRTX1133), 9O0O (KRAS (1-169)GMPPNP with MRTX1133), 9O0P (MRASmut(1-178)GDP with MRTX1133), and 9O0Q (MRASmut(1-178)GMPPNP with MRTX1133). The structures used as initial models for molecular replacement are available in the PDB under accession codes 1X1R (MRAS), 7RPZ (KRAS(G12D)GDP-MRTX1133), and 7TVF (SMP complex). Structures utilized for superpositions, and analysis can be found in the PDB using accession codes 1NVU (HRAS-SOS1), 6OB2 (KRAS + NF1), 6XI7 (KRAS-CRAF), 7LC1 (KRAS-Sin1), 7RPZ (KRAS(G12D)GDP-MRTX1133), 7T47 (KRAS(G12D)GMPPCP-MRTX1133), 7TVF (SMP complex), 8B69 (KRAS-Rgl2), 9AX6 (KRAS-RMC6236-CypA) and 9C15 (KRAS-PI3Kα). The source data underlying Figs. 1d, 5a, 5c, 6a–b, 7b, 7d and 7f–i and Supplementary Figs. 5a, 5g, 6a–b, 7b–c, 8e, 9 and 10 are provided as a Source Data file. Source data are provided with this paper.
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Acknowledgements
We acknowledge Dominic Esposito, William Gillette, John-Paul Denson, Matt Drew, Peter H. Frank, Natalie Granato-Guerrero, Brianna Higgins, Min Hong, Jenna Hull, Jennifer Mehalko, Simon Messing, Ashley Mitchell, Shelley Perkins, Ivy Poon, Nitya Ramakrishnan, Katie Geis, Mukul Sherekar, Troy Taylor, and Nicolas Wright for production of protein reagents used in this work. We thank Timothy Waybright for performing the nucleotide exchange analysis. CryoEM data were collected at the NCI National Cryo−EM Facility at the Frederick National Laboratory for Cancer Research, and we thank Tara Fox and Thomas Edwards for their help with the data collection. RASless cells were generated by Matthew J. Sale and Madeleine R. Allison. The authors also acknowledge the use of the Frederick Research Computing Environment (FRCE). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. This work is based upon research conducted at the NECAT beamlines, which are funded by the NIGMS/NIH (P30 GM124165). This research was supported by an agreement between the Advanced Photon Source and the Diamond Light Source, the U.K.‘s national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire, where the work was performed under proposal AU34315-3. This project was funded in part with federal funds from the National Cancer Institute, National Institutes of Health (NIH) Contract 75N91019D00024. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, and the mention of trade names, commercial products, or organizations does not imply endorsement by the US Government.
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D.A.B. and D.K.S. initiated the project. D.A.B. prepared the cryo-EM sample. L.I.F. and J.R.P. performed negative stain EM, cryo-EM grid preparation, data collection, processing, model building, refinement, and analysis. T.S. produced in-house graphene oxide grids. J.F. helped with the image processing. L.C.Y. and R.G. prepared and performed cellular experiments. D.A.B. conducted crystallography, structural analysis, and ITC experiments. V.E.W. and K.R.G. helped with the cloning and preparation of recombinant proteins. D.A.B., L.C.Y., D.V.N., F.M., and D.K.S. contributed to experimental design and data analysis. D.A.B., L.I.F., and D.K.S. wrote the manuscript with input from all authors.
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F.M. is a consultant for Ideaya Biosciences, Kura Oncology, Leidos Biomedical Research, Pfizer, Daiichi Sankyo, Amgen, PMV Pharma, OPNA-IO, and Quanta Therapeutics. He has received research grants from Boehringer–Ingelheim, and is a consultant for and cofounder of BridgeBio Pharma. The remaining authors declare no competing interests.
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Bonsor, D.A., Finci, L.I., Potter, J.R. et al. Structure of SHOC2-KRAS-PP1C complex reveals RAS isoform-specific determinants and insights into targeting complex assembly by RAS inhibitors. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68319-1
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DOI: https://doi.org/10.1038/s41467-026-68319-1
