Abstract
Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30-10 A range and sometimes even beyond 10 A. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/.
Highlights
The three-dimensional structure of a macromolecular complex provides important information about the intricate interactions between its components
Some macromolecular complexes have been produced in homogeneous form, crystallized and analyzed at high resolution (3–2 Aor better) using X-ray crystallography (XR)
We found that the so-called ‘R factor’ widely used in crystallography and specific to reciprocal space, P jjFhemj À jFhmodjj
Summary
The three-dimensional structure of a macromolecular complex provides important information about the intricate interactions between its components. A variety of algorithms are currently implemented, including CoAn (Volkmann & Hanein, 1999), DockEM (Roseman, 2000), EMfit (Rossmann, 2000), Foldhunter (Jiang et al, 2001), Situs (Wriggers et al, 1999), 3SOM (Ceulemans & Russell, 2004) and URO (Navaza et al, 2002) Careful use of such packages enhances the information that can be gained from the fitting compared with a manual docking procedure and allows errors to be estimated using criteria other than the human eye. The resulting fitting procedure can be cumbersome, especially in difficult cases in which numerical criteria do not unambiguously discern the correct solution This often occurs when some atomic structures to be fitted into the EM map are not available, leaving unaccounted-for density (Lescar et al, 2001). Normal-mode calculations based on NORMA (Suhre et al, 2006) are available in UROX
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