7TB3

cryo-EM structure of MBP-KIX-apoferritin

Summary for 7TB3

• Entry DOI: 10.2210/pdb7tb3/pdb
• EMDB information: 25791
• Descriptor: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed (1 entity in total)
• Functional Keywords: protein engineering, simulation, peptide therapeutics, acute myeloid leukemia, structural protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 24
• Total formula weight: 729802.51

Authors

Zhang, K.,Horikoshi, N.,Li, S.,Powers, A.,Hameedi, M.,Pintilie, G.,Chae, H.,Khan, Y.,Suomivuori, C.,Dror, R.,Sakamoto, K.,Chiu, W.,Wakatsuki, S. (deposition date: 2021-12-21, release date: 2022-03-16, Last modification date: 2024-10-23)

Primary citation

Zhang, K.,Horikoshi, N.,Li, S.,Powers, A.S.,Hameedi, M.A.,Pintilie, G.D.,Chae, H.D.,Khan, Y.A.,Suomivuori, C.M.,Dror, R.O.,Sakamoto, K.M.,Chiu, W.,Wakatsuki, S.
Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia.
Acs Cent.Sci., 8:214-222, 2022

PubMed Abstract: Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures of proteins that are flexible and smaller than 30 kDa. The 11 kDa KIX domain of CREB-binding protein (CBP), a potential therapeutic target for acute myeloid leukemia and other cancers, is a protein which has defied structure-based inhibitor design. Here, we develop an experimental approach to overcome the size limitation by engineering a protein double-shell to sandwich the KIX domain between apoferritin as the inner shell and maltose-binding protein as the outer shell. To assist homogeneous orientations of the target, disulfide bonds are introduced at the target-apoferritin interface, resulting in a cryo-EM structure at 2.6 Å resolution. We used molecular dynamics simulations to design peptides that block the interaction of the KIX domain of CBP with the intrinsically disordered pKID domain of CREB. The double-shell design allows for fluorescence polarization assays confirming the binding between the KIX domain in the double-shell and these interacting peptides. Further cryo-EM analysis reveals a helix-helix interaction between a single KIX helix and the best peptide, providing a possible strategy for developments of next-generation inhibitors.

PubMed: 35233453
DOI: 10.1021/acscentsci.1c01090

Experimental method

ELECTRON MICROSCOPY (2.57 Å)