DeepMind presented remarkably accurate predictions at the recent CASP14 protein structure prediction assessment conference. We explored network architectures incorporating related ideas and obtained the best performance with a three-track network in which information at the 1D sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging X-ray crystallography and cryo-EM structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short circuiting traditional approaches which require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.

Summary The mammalian Target of Rapamycin Complex 1 (mTORC1) regulates cell growth in response to the nutrient and energy status of the cell, and its deregulation is common in human cancers. Little is known about the overall architecture and subunit organization of this essential signaling complex. We have determined the three-dimensional (3D) structure of the fully assembled human mTORC1 by cryo-electron microscopy (cryo-EM). Our analyses reveal that mTORC1 is an obligate dimer with an overall rhomboid shape and a central cavity. The dimeric interfaces are formed by interlocking interactions between the mTOR and raptor subunits. Extended incubation with FKBP12-rapamycin compromises the structural integrity of mTORC1 in a stepwise manner, leading us to propose a model in which rapamycin inhibits mTORC1-mediated phosphorylation of 4E-BP1 and S6K1 through different mechanisms.

The type III secretion system (T3SS) is a macromolecular ‘injectisome’, that allows bacterial pathogens to transport virulence proteins into the eukaryotic host cell. This macromolecular complex is constituted by connected ring-like structures that span both bacterial membranes. The crystal structures of the periplasmic domain of the outer membrane (OM) secretin EscC and the inner membrane (IM) protein PrgH reveal the conservation of a modular fold among the three proteins which form the OM and IM rings of the T3SS. This leads to the hypothesis that this conserved fold provides a common ring-building motif that allows for the assembly of the variably sized OM and IM rings characteristic of the T3SS. Utilizing an integrated structural and experimental approach, ring-models for the periplasmic domain of EscC were generated and placed in the context of the assembled T3SS, providing evidence for direct interaction between the OM and IM ring components and an unprecedented span of the OM secretin.