Modeling protein structure at near atomic resolutions with Gorgon

Abstract

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.

Heterodimers as the Structural Unit of the T=1 Capsid of the Fungal Double-Stranded RNA Rosellinia necatrix Quadrivirus 1

“…To test whether the selected density corresponded to a single asymmetric unit, the complete capsid map was restored in each cycle after applying icosahedral symmetry to the selected density. The secondary-structure elements (SSE) in the RnQV1 density were identified and modeled using the SSEHunter program (42) integrated in the Gorgon software (43). For difference map calculations, spherically averaged radial density profiles were calculated, normalized, and scaled to match the fit between the cryo-EM map and quasi-atomic model profiles.…”

Cryphonectria nitschkei Virus 1 Structure Shows that the Capsid Protein of Chrysoviruses Is a Duplicated Helix-Rich Fold Conserved in Fungal Double-Stranded RNA Viruses

“…CP subunits (and their halves) were segmented using Chimera and were iteratively refined to avoid subunit overlap or loose density. Capsid protein secondary structure elements (SSE) were identified using Gorgon (2). Various SSE prediction methods of the CnV1 and PcV CP sequences were used to test correlation with our structural subunit model (10).…”

A Newly Isolated Reovirus Has the Simplest Genomic and Structural Organization of Any Reovirus

“…For each protein in the asymmetric unit, a subvolume extending 20 Å out from the location of its closest structurally characterized homolog from CPV was extracted. Gorgon was then used to automatically skeletonize density and to manually identify secondary structural elements in the extracted subvolume (29,30).…”