3V1C
Crystal structure of de novo designed MID1-zinc
Summary for 3V1C
| Entry DOI | 10.2210/pdb3v1c/pdb |
| Related | 1YZM 3V1A 3V1B 3V1D 3V1E 3V1F |
| Descriptor | Computational design, MID1-zinc, ZINC ION, L(+)-TARTARIC ACID, ... (5 entities in total) |
| Functional Keywords | helix-turn-helix, metal binding, homodimer, metal binding protein, hydrolase, de novo protein |
| Biological source | ARTIFICIAL GENE |
| Total number of polymer chains | 2 |
| Total formula weight | 11279.14 |
| Authors | Der, B.S.,Machius, M.,Miley, M.J.,Kuhlman, B. (deposition date: 2011-12-09, release date: 2012-01-11, Last modification date: 2023-09-13) |
| Primary citation | Der, B.S.,Machius, M.,Miley, M.J.,Mills, J.L.,Szyperski, T.,Kuhlman, B. Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J.Am.Chem.Soc., 134:375-385, 2012 Cited by PubMed Abstract: Computationally designing protein-protein interactions with high affinity and desired orientation is a challenging task. Incorporating metal-binding sites at the target interface may be one approach for increasing affinity and specifying the binding mode, thereby improving robustness of designed interactions for use as tools in basic research as well as in applications from biotechnology to medicine. Here we describe a Rosetta-based approach for the rational design of a protein monomer to form a zinc-mediated, symmetric homodimer. Our metal interface design, named MID1 (NESG target ID OR37), forms a tight dimer in the presence of zinc (MID1-zinc) with a dissociation constant <30 nM. Without zinc the dissociation constant is 4 μM. The crystal structure of MID1-zinc shows good overall agreement with the computational model, but only three out of four designed histidines coordinate zinc. However, a histidine-to-glutamate point mutation resulted in four-coordination of zinc, and the resulting metal binding site and dimer orientation closely matches the computational model (Cα rmsd = 1.4 Å). PubMed: 22092237DOI: 10.1021/ja208015j PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.129 Å) |
Structure validation
Download full validation report
