ArticleActa crystallographica. Section D, Biological crystallography2009
UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions.
Article in Acta crystallographica. Section D, Biological crystallography, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 30 citations in OpenAlex.
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.Acta crystallographica. Section D, Structural biology · 2016Article
- Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA.Scientific reports · 2016Article
- Structural rearrangements in the phage head-to-tail interface during assembly and infection.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Article
- Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles.Journal of molecular biology · 2013Article
- A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.Nature structural & molecular biology · 2012Article
- Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography.Advances in experimental medicine and biology · 2012Review
- Extracellular complexes of the hematopoietic human and mouse CSF-1 receptor are driven by common assembly principles.Structure (London, England : 1993) · 2011Article
- Quaternary structure of the specific p53-DNA complex reveals the mechanism of p53 mutant dominance.Nucleic acids research · 2011Article
- Modeling protein structure at near atomic resolutions with Gorgon.Journal of structural biology · 2011Article
- Matching structural densities from different biophysical origins with gain and bias.Journal of structural biology · 2011Article
- Exploring the spatial and temporal organization of a cell's proteome.Journal of structural biology · 2011Review
- Structure of lactococcal phage p2 baseplate and its mechanism of activation.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Analyses of subnanometer resolution cryo-EM density maps.Methods in enzymology · 2010Article
- The Max-Inf2/Lorentz Center workshop on New algorithms in macromolecular crystallography and electron microscopy.Acta crystallographica. Section D, Biological crystallography · 2009Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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/.
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