21DH
Crystal structure of MBP-fused Monobody P' in complex with HPPU
This is a non-PDB format compatible entry.
Summary for 21DH
| Entry DOI | 10.2210/pdb21dh/pdb |
| Related PRD ID | PRD_900018 |
| Descriptor | Maltose/maltodextrin-binding periplasmic protein,Monobody P', alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose, 1-(4-hydroxyphenyl)-3-phenyl-urea, ... (4 entities in total) |
| Functional Keywords | engineered binding protein, fibronectin type iii domain, ligand-binding complex, beta-sandwich fold, cell adhesion |
| Biological source | Escherichia coli K-12 More |
| Total number of polymer chains | 6 |
| Total formula weight | 326832.24 |
| Authors | Endo, K.,Umemoto, S.,Okumura, H.,Sato, Y.,Tsukiji, S.,Nagano, S.,Murakami, H.,Hino, T. (deposition date: 2025-12-09, release date: 2026-03-18) |
| Primary citation | Endo, K.,Umemoto, S.,Tsuzuki, N.,Okumura, H.,Sato, Y.,Yoshii, T.,Tsukiji, S.,Nagano, S.,Murakami, H.,Hino, T. Crystallization and X-ray structure of a highly aggregation-prone monobody engineered for high-affinity small-molecule recognition. Acta Crystallogr.,Sect.F, 82:75-82, 2026 Cited by PubMed Abstract: Monobodies, engineered protein scaffolds derived from the fibronectin type III domain, are powerful alternatives to conventional antibodies. While the native scaffold is robust, engineering the variable loops can often compromise solubility and promote aggregation. Here, we report the crystallization and structure determination at 2.57 Å resolution of a monobody (Mb-P') engineered to bind the synthetic small molecule HPPU [1-(4-hydroxyphenyl)-3-phenylurea] with nanomolar affinity. Although Mb-P' exhibited severe polydispersity and heterogeneous oligomerization in solution, N-terminal fusion with maltose-binding protein (MBP) using an optimized linker successfully yielded monodisperse species and diffraction-quality crystals. The crystal structure exhibited pseudo-D symmetry in the asymmetric unit, in which the MBP moiety interacts with and partially covers the F and G β-strands of the monobody. This steric masking suggests that MBP acts as a solubility enhancer by shielding the aggregation-prone surface patches generated by loop engineering. Our results demonstrate that this fusion strategy effectively enables structural studies of aggregation-prone proteins obtained from engineered scaffolds. PubMed: 41660693DOI: 10.1107/S2053230X26000798 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.57 Å) |
Structure validation
Download full validation report
