9IRV
MultiBody Refinement of dimeric DARPin and its bound GFP on a symmetric scaffold
Summary for 9IRV
| Entry DOI | 10.2210/pdb9irv/pdb |
| EMDB information | 60822 61130 |
| Descriptor | DARPin, Green fluorescent protein (2 entities in total) |
| Functional Keywords | darpin, dimeric, gfp, scaffold, biosynthetic protein |
| Biological source | synthetic construct More |
| Total number of polymer chains | 3 |
| Total formula weight | 113161.12 |
| Authors | |
| Primary citation | Lu, X.,Yan, M.,Cai, Y.,Song, X.,Chen, H.,Du, M.,Wang, Z.,Li, J.,Niu, L.,Zeng, F.,Hao, Q.,Zhang, H. A large, general and modular DARPin-apoferritin scaffold enables the visualization of small proteins by cryo-EM. Iucrj, 12:393-402, 2025 Cited by PubMed Abstract: Single-particle cryo-electron microscopy (cryo-EM) has emerged as an indispensable technique in structural biology that is pivotal for deciphering protein architectures. However, the medium-sized proteins (30-40 kDa) that are prevalent in both eukaryotic and prokaryotic organisms often elude the resolving capabilities of contemporary cryo-EM methods. To address this challenge, we engineered a scaffold strategy that securely anchors proteins of interest to a robust, symmetric base via a selective adapter. Our most efficacious constructs, namely models 4 and 6c, feature a designed ankyrin-repeat protein (DARPin) rigidly linked to an octahedral human apoferritin via a helical linker. By utilizing these large, highly symmetric scaffolds (∼1 MDa), we achieved near-atomic-resolution cryo-EM structures of green fluorescent protein (GFP) and maltose-binding protein (MBP), revealing nearly all side-chain densities of GFP and the distinct structural features of MBP. The modular design of our scaffold allows the adaptation of new DARPins through minor amino-acid-sequence modifications, enabling the binding and visualization of a diverse array of proteins. The high symmetry and near-spherical shape of the scaffold not only mitigates the prevalent challenge of preferred particle orientation in cryo-EM but also significantly reduces the demands of image collection and data processing. This approach presents a versatile solution, breaking through the size constraints that have traditionally limited single-particle cryo-EM. PubMed: 40277178DOI: 10.1107/S2052252525003021 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.47 Å) |
Structure validation
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