Situs: A Package for Docking Crystal Structures into Low-Resolution Maps from Electron Microscopy

Abstract

Three-dimensional image reconstructions of largescale protein aggregates are routinely determined by electron microscopy (EM). We combine lowresolution EM data with high-resolution structures of proteins determined by x-ray crystallography. A set of visualization and analysis procedures, termed the Situs package, has been developed to provide an efficient and robust method for the localization of protein subunits in low-resolution data. Topologyrepresenting neural networks are employed to vector-quantize and to correlate features within the structural data sets. Microtubules decorated with kinesin-related ncd motors are used as model aggregates to demonstrate the utility of this package of routines. The precision of the docking has allowed for the extraction of unique conformations of the macromolecules and is limited only by the reliability of the underlying structural data. Academic Press

The Subnanometer Resolution Structure of the Glutamate Synthase 1.2-MDa Hexamer by Cryoelectron Microscopy and Its Oligomerization Behavior in Solution

“…To perform the fitting of atomic data into the cryo-EM map, the following programs were compared: (i) rigid body fitting in Fourier space with Colores and Colacor algorithms of SITUS (46,47); (ii) real space fitting with the FoldHunterP algorithm of EMAN (48,49); (iii) real space fitting using the operation "Fit Model in Map" of Chimera (50,51). A first ␣ 2 dimer was fitted, and the 3-fold symmetry was used to calculate the atomic coordinates of the other two.…”

“…1D), specific for a 322 point group symmetry. Second, using the rigid body fitting techniques of SITUS (46,47) and EMAN (48,49) software, it was easy to fit the atomic structure of the crystallographic ␣ 2 dimers (Protein Data Bank code 1ea0 (9)) forming three large "pillars" within the complex (Fig. 1, C and D).…”

Chapter 13 Visualization of Dynamins

“…The GTPase and PH crystal structures of dynamin were docked into the 3-dimensional density maps of dynamin using YAMMP/YUP and revealed a possible corkscrew mechanism of constriction (Mears et al , 2007). Another docking package, SITUS, uses vector quantization to fit high-resolution structures into low-resolution density (Wriggers et al, 1999). This method allows for fast and exhaustive docking of rigid-body atomic structures to the cryo-EM structure, and new methods allow for flexible fitting as well (Wriggers and Birmanns, 2001).…”

Interpretation of electron density with stereographic roadmap projections

“…Various programs have been developed to help analyze higher resolution cryo-EM results. These include programs for the fitting of X-ray crystallographically determined structures into cryo-EM densities (Roseman, 2000;Rossmann et al, 2001;Volkmann and Hanein, 2003;Wriggers et al, 1999) and programs for the visualization of macromolecules in cryo-EM density maps (Gillet et al, 2005;Pettersen et al, 2004). Nevertheless, interpretation of the final results of cryo-EM reconstructions can sometimes be helped by alternate methods of presentation.…”