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TitleHigh-resolution cryo-EM structures of small protein-ligand complexes near the theoretical size limit.
Journal, issue, pagesNat Commun, Year 2026
Publish dateApr 14, 2026
AuthorsKunwoong Park / Youngki Yoo / Hyunbum Jeon / Kiju Choi / Hanseong Kim / Eunju Kwon / Hyun-Ho Lim / Dong Young Kim / Kyoung Tai No /
PubMed AbstractCryo-electron microscopy (cryo-EM) is a widely used technique for determining macromolecular structures at near-atomic resolution. The theoretical lower limit of particle sizes suitable for cryo-EM ...Cryo-electron microscopy (cryo-EM) is a widely used technique for determining macromolecular structures at near-atomic resolution. The theoretical lower limit of particle sizes suitable for cryo-EM structural analysis is estimated to be 38 kDa; typical constraints involve factors such as image contrast and particle alignment accuracy. In this study, we present cryo-EM structures of two protein-ligand complexes near this lower size threshold. First, the structure of the maltose-binding protein complexed with maltose, with a structurally ordered mass of 40.8 kDa, was determined at a resolution of 2.4 Å; both the maltose and water molecules were clearly identified in this structure. The second structure was the kinase domain of human PLK1 complexed with onvansertib, with a structurally ordered mass of 31.6 kDa, below the theoretical 38 kDa limit; this domain was determined at a resolution of 3.4 Å using a gold-supported grid in the presence of β-octyl-glucoside. The density map clearly shows the backbone of PLK1 secondary structure, and the onvansertib. These results demonstrate that cryo-EM can be effectively employed to determine structures of small proteins or domains, and to perform structure-based drug screening for small proteins, without requiring structural fiducials for particle alignment.
External linksNat Commun / PubMed:41980966
MethodsEM (single particle)
Resolution2.35 - 3.38 Å
Structure data

66973

9xko

EMDB-66973, PDB-9xko:
High-resolution cryo-EM structure of Maltose Binding Protein
Method: EM (single particle) / Resolution: 2.35 Å

68616

22rd

EMDB-68616, PDB-22rd:
High-resolution cryo-EM structure of human Polo-like kinase 1 in complex with onvansertib
Method: EM (single particle) / Resolution: 3.38 Å

Chemicals

ChemComp-937:
1-(2-HYDROXYETHYL)-8-[[5-(4-METHYLPIPERAZIN-1-YL)-2-(TRIFLUOROMETHOXY)PHENYL]AMINO]-4,5-DIHYDROPYRIMIDO[5,4-G]INDAZOLE-3-CARBOXAMIDE

ChemComp-HOH:
WATER

Source
  • escherichia coli (E. coli)
  • homo sapiens (human)
KeywordsTRANSFERASE / small protein-ligand complex / SUGAR BINDING PROTEIN

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