9I5E

A Coiled Coil Module Strategy for High-Resolution Cryo-EM Structures of Small Proteins for Drug Discovery

Summary for 9I5E

• Entry DOI: 10.2210/pdb9i5e/pdb
• EMDB information: 52628
• Descriptor: Isoform 2B of GTPase KRas,APH2, Nanobody 26, {(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2S)-2-fluoropropanoyl]piperazin-2-yl}acetonitrile, ... (5 entities in total)
• Functional Keywords: cryoem imaging scaffold, cancer, gtpase, nanobodies, coiled-coil, structural protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 76196.29

Authors

Samson, C.,Dossou, I.,Steinmetz, A.,Kumar, A.,Mathieu, M.,Rak, A. (deposition date: 2025-01-28, release date: 2025-11-12, Last modification date: 2026-05-27)

Primary citation

Camille, S.,Irene, D.,Anke, S.,Anand, K.,Magali, M.,Alexey, R.
Structural determination of small proteins by cryo-EM using a coiled coil module strategy.
Sci Rep, 15:36800-36800, 2025

PubMed Abstract: Electron cryo-microscopy (Cryo-EM) has traditionally been used for structural determination of proteins larger than 50 kDa. Recently, various approaches, such as fusion to a scaffold or the use of DARPins-cages, have been developed to extend its application to smaller proteins. In this study, we determined the structure of the small protein target kRasG12C by fusing it to the coiled-coil motif APH, which is targeted by several nanobodies. This method enabled us to achieve a structure with atomic details at a resolution of 3.7 Å. The kRasG12C structure was bound to the inhibitor drug MRTX849 and GDP, both clearly visible in the density map. This method is advantageous due to its ease of setup and applicability to other targets. Additionally, we investigated several other techniques that can be applied to small proteins, regardless of the presence of a terminal helix. These advancements demonstrate the potential of cryo-EM for detailed structural analysis of a wide range of protein targets, extending cryo-EM application for drug discovery.

PubMed: 41120715
DOI: 10.1038/s41598-025-20608-3

Experimental method

ELECTRON MICROSCOPY (3.77 Å)