UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions

UROX is software designed for the interactive fitting of atomic models into electron-microscopy reconstructions. The main features of the software are presented, along with a few examples.

[1]  Helen R Saibil,et al.  An expanded protein folding cage in the GroEL-gp31 complex. , 2006, Journal of molecular biology.

[2]  Glaucius Oliva,et al.  Fast Rigid-Body Refinement for Molecular-Replacement Techniques , 1992 .

[3]  Eaton E. Lattman,et al.  Optimal sampling of the rotation function , 1972 .

[4]  J. Lepault,et al.  Visualization of the Target-Membrane-Inserted Fusion Protein of Semliki Forest Virus by Combined Electron Microscopy and Crystallography , 2003, Cell.

[5]  Graeme Wistow,et al.  Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. , 2006, Structure.

[6]  M. Delarue,et al.  On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[7]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[8]  B. Gowen,et al.  Multiple distinct assemblies reveal conformational flexibility in the small heat shock protein Hsp26. , 2006, Structure.

[9]  E. Orlova,et al.  Dodecameric Structure of the Small Heat Shock Protein Acr1 from Mycobacterium tuberculosis* , 2005, Journal of Biological Chemistry.

[10]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[11]  J. Mccammon,et al.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. , 1999, Journal of structural biology.

[12]  D. Stuart,et al.  Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex , 2007, Proceedings of the National Academy of Sciences.

[13]  V. Georgiev.  Virology , 1955, Nature.

[14]  Magali Mathieu,et al.  Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion , 2001, The EMBO journal.

[15]  A. Roseman.  Docking structures of domains into maps from cryo-electron microscopy using local correlation. , 2000, Acta crystallographica. Section D, Biological crystallography.

[16]  William H. Press,et al.  Numerical Recipes: FORTRAN , 1988 .

[17]  良二 上田.  J. Appl. Cryst.の発刊に際して , 1970 .

[18]  Stephen D Fuller,et al.  Cryo-Electron Tomographic Structure of an Immunodeficiency Virus Envelope Complex In Situ , 2006, PLoS pathogens.

[19]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[20]  A. Klug,et al.  Physical principles in the construction of regular viruses. , 1962, Cold Spring Harbor symposia on quantitative biology.

[21]  J. Lepault,et al.  Structure of birnavirus-like particles determined by combined electron cryomicroscopy and X-ray crystallography. , 2005, The Journal of general virology.

[22]  Niels Volkmann,et al.  Docking of atomic models into reconstructions from electron microscopy. , 2003, Methods in enzymology.

[23]  P. Adams,et al.  Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution , 1995, Nature Structural Biology.

[24]  R. Ruigrok,et al.  An Archaeal Peptidase Assembles into Two Different Quaternary Structures , 2006, Journal of Biological Chemistry.

[25]  J. Lepault,et al.  Structural Peptides of a Nonenveloped Virus Are Involved in Assembly and Membrane Translocation , 2005, Journal of Virology.

[26]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[27]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[28]  M. Yeager,et al.  Structural determinants of rotavirus subgroup specificity mapped by cryo-electron microscopy. , 2006, Journal of molecular biology.

[29]  Irina Gutsche,et al.  The Birnavirus Crystal Structure Reveals Structural Relationships among Icosahedral Viruses , 2005, Cell.

[30]  J Navaza,et al.  Structural polymorphism of the major capsid protein of rotavirus , 2001, The EMBO journal.

[31]  R. Ruigrok,et al.  Structure of the dodecahedral penton particle from human adenovirus type 3. , 2006, Journal of molecular biology.

[32]  M. S. Chapman,et al.  Fitting of high-resolution structures into electron microscopy reconstruction images. , 2005, Structure.

[33]  Karsten Suhre,et al.  NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. , 2006, Acta crystallographica. Section D, Biological crystallography.

[34]  D. Stuart,et al.  Crystal structure of a soluble CD28-Fab complex , 2005, Nature Immunology.

[35]  J. Escaig,et al.  Structure of rotaviruses as studied by the freeze-drying technique. , 1979, Virology.

[36]  S. Cusack,et al.  A quasi‐atomic model of human adenovirus type 5 capsid , 2005, The EMBO journal.

[37]  R. Russell,et al.  Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization. , 2004, Journal of molecular biology.

[38]  J. Lepault,et al.  Electronic Reprint Biological Crystallography on the Fitting of Model Electron Densities into Em Reconstructions: a Reciprocal-space Formulation , 2022 .

[39]  J. Navaza,et al.  The Fusion Glycoprotein Shell of Semliki Forest Virus An Icosahedral Assembly Primed for Fusogenic Activation at Endosomal pH , 2001, Cell.

[40]  Konrad Hinsen,et al.  Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. , 2005, Biophysical journal.

[41]  A. Hoenger,et al.  Structural rearrangements in tubulin following microtubule formation , 2005, EMBO reports.

[42]  A. Hoenger,et al.  Complex formation with kinesin motor domains affects the structure of microtubules. , 2004, Journal of molecular biology.

[43]  M. Baker,et al.  Bridging the information gap: computational tools for intermediate resolution structure interpretation. , 2001, Journal of molecular biology.

[44]  Wei Zhang,et al.  Combining X-Ray Crystallography and Electron Microscopy , 2005, Structure.

[45]  B. Trus,et al.  Infectious Bursal Disease Virus Capsid Assembly and Maturation by Structural Rearrangements of a Transient Molecular Switch , 2007, Journal of Virology.

[46]  J. Lepault,et al.  Geometric Mismatches within the Concentric Layers of Rotavirus Particles: a Potential Regulatory Switch of Viral Particle Transcription Activity , 2008, Journal of Virology.

[47]  R. Matadeen,et al.  The Dynamics of Signal Triggering in a gp130-Receptor Complex , 2007, Structure.

[48]  David I. Stuart,et al.  A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting , 2006, Nature.

[49]  Jorge Navaza.  On the computation of structure factors by FFT techniques. , 2002, Acta crystallographica. Section A, Foundations of crystallography.

[50]  F. Liprandi,et al.  The structure of the rotavirus inner capsid studied by electron microscopy of chemically disrupted particles. , 1986, The Journal of general virology.

[51]  John E. Johnson,et al.  Identification of a Fab interaction footprint site on an icosahedral virus by cryoelectron microscopy and X-ray crystallography , 1992, Nature.

[52]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[53]  C El-Bez,et al.  Cryo-negative staining reduces electron-beam sensitivity of vitrified biological particles. , 2002, Journal of structural biology.

[54]  J. Conway,et al.  Human kinetochore-associated kinesin CENP-E visualized at 17 A resolution bound to microtubules. , 2006, Journal of molecular biology.

[55]  H. Saibil,et al.  Allosteric signaling of ATP hydrolysis in GroEL–GroES complexes , 2006, Nature Structural &Molecular Biology.

[56]  N. Volkmann,et al.  Quantitative fitting of atomic models into observed densities derived by electron microscopy. , 1999, Journal of structural biology.

[57]  M. Rossmann,et al.  Fitting atomic models into electron-microscopy maps. , 2000, Acta crystallographica. Section D, Biological crystallography.

[58]  P. Stewart,et al.  Difference imaging of adenovirus: bridging the resolution gap between X‐ray crystallography and electron microscopy. , 1993, The EMBO journal.