De Novo Atomic Protein Structure Modeling for Cryo-EM Density Maps Using 3D Transformer and Hidden Markov Model

Accurately building three-dimensional (3D) atomic structures from 3D cryo-electron microscopy (cryo-EM) density maps is a crucial step in the cryo-EM-based determination of the structures of protein complexes. Despite improvements in the resolution of 3D cryo-EM density maps, the de novo conversion of density maps into 3D atomic structures for protein complexes that do not have accurate homologous or predicted structures to be used as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated ab initio cryo-EM structure modeling method that utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps first, and then employs a novel Hidden Markov Model (HMM) to connect predicted atoms to build backbone structures of proteins. Tested on a standard test dataset of 128 cryo-EM density maps with varying resolutions (2.1 - 5.6 °A) and different numbers of residues (730 - 8,416), Cryo2Struct built substantially more accurate and complete protein structural models than the widely used ab initio method - Phenix in terms of multiple evaluation metrics. Moreover, on a new test dataset of 500 recently released density maps with varying resolutions (1.9 - 4.0 °A) and different numbers of residues (234 - 8,828), it built more accurate models than on the standard dataset. And its performance is rather robust against the change of the resolution of density maps and the size of protein structures.