8V9O
Imaging scaffold engineered to bind the therapeutic protein target BARD1
Summary for 8V9O
| Entry DOI | 10.2210/pdb8v9o/pdb |
| Descriptor | Tetrahedral Nanocage Cage, Non-Fusion Component, Tetrahedral Nanocage Cage Component Fused to Anti-BARD1 Darpin, CALCIUM ION (3 entities in total) |
| Functional Keywords | nanohedra, protein cage, tetrahedral, darpin, imaging scaffold, de novo protein |
| Biological source | synthetic construct More |
| Total number of polymer chains | 6 |
| Total formula weight | 165799.14 |
| Authors | Agdanowski, M.P.,Castells-Graells, R.,Sawaya, M.R.,Yeates, T.O.,Arbing, M.A. (deposition date: 2023-12-08, release date: 2024-05-15, Last modification date: 2024-06-12) |
| Primary citation | Agdanowski, M.P.,Castells-Graells, R.,Sawaya, M.R.,Cascio, D.,Yeates, T.O.,Arbing, M.A. X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation. Acta Crystallogr.,Sect.F, 80:107-115, 2024 Cited by PubMed Abstract: Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage-cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications. PubMed: 38767964DOI: 10.1107/S2053230X2400414X PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.81 Å) |
Structure validation
Download full validation report
