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Exploring Icosahedral Virus Structures with Viper REVIEWS EXPLORING ICOSAHEDRAL VIRUS STRUCTURES WITH VIPER Padmaja Natarajan, Gabriel C. Lander, Craig M. Shepherd, Vijay S. Reddy, Charles L. Brooks III and John E. Johnson Abstract | Virus structures are megadalton nucleoprotein complexes with an exceptional variety of protein–protein and protein–nucleic-acid interactions. Three-dimensional crystal structures of over 70 virus capsids, from more than 20 families and 30 different genera of viruses, have been solved to near-atomic resolution. The enormous amount of information contained in these structures is difficult to access, even for scientists trained in structural biology. Virus Particle Explorer (VIPER) is a web-based catalogue of structural information that describes the icosahedral virus particles. In addition to high-resolution crystal structures, VIPER has expanded to include virus structures obtained by cryo-electron microscopy (EM) techniques. The VIPER database is a powerful resource for virologists, microbiologists, virus crystallographers and EM researchers. This review describes how to use VIPER, using several examples to show the power of this resource for research and educational purposes. ASYMMETRIC UNIT A wealth of virus-structure information that is useful virus structures or a family of virus structures by visit- The asymmetric unit of an to virologists can be derived from the coordinates of ing the ‘Visual VIPER’ tool from the ‘Utilities/Tools’ icosahedral virus structure is high-resolution icosahedral virus structures depos- section of the VIPER main menu. A researcher can defined as the smallest part of ited in the Protein Data Bank (PDB)1. However, it use the same tool to compare these viruses at various the structure from which the complete structure of the virus can be a challenging task — even for experienced levels of protein-subunit organization in their capsid can be built using a specific set structural biologists — to obtain information such as shells. Similarly, a beginner in structural virology can of 60 rotational matrices that protein–protein interactions that requires multiple use the tool ‘Icosahedral Server’ as an informative describe the 5:3:2 symmetry of ASYMMETRIC UNITS of the symmetric particles. This need means for building paper models of quasi-equivalent the virus particle. led to the creation of Virus Particle Explorer (VIPER)2, a virus capsids. The same location provides an explana- web-based information centre that placed all the virus- tion of the geometric principles of quasi-equivalence subunit coordinates deposited in the PDB into a single theory and its application to larger virus capsids. standard orientation. This enabled easy comparisons After characterizing a new virus and assigning among the structures and facilitated the sub sequent it to a family based on genome-sequence similarity, development of visualization and computational tools an investigator can use VIPER to determine whether to deal with icosahedral nucleoprotein particles. The structural similarities exist with related viruses in the visualizations and derived structural information database. For example, a virologist working on the bio- for each virus are organized to help students and logical aspects of a new picornavirus can gather infor- Department of Molecular researchers understand the details of virus structures. mation on all the related structures belonging to the Biology, The Scripps A first-time visitor to VIPER is led through the Picornaviridae from VIPER by first visiting the ‘Name Research Institute, La Jolla, details of the various aspects of the site by clicking Index’ page and listing the viruses by family, or by using California 92037, USA. Correspondence to J.E.J. the ‘First Time Users’ link available from every page the search tool ‘Find a Virus’ to access the structures of e-mail: [email protected] of the website. One can enter the world of viruses with interest. The user can then visually compare this same doi:10.1038/nrmicro1247 the display of a gallery of user-selected individual set of structures with the ‘Visual VIPER’ tool to study NATURE REVIEWS | MICROBIOLOGY VOLUME 3 | OCTOBER 2005 | 809 © 2005 Nature Publishing Group REVIEWS VIPER PDB to VIPER conversion Cryo-EM structures Crystal structures Data & Analysis Utilities/Tools Search/Help Name Index Crystallization Conditions Icosahedral Server Quick Search T Index Crystal Parameters Map a Residue Find a Virus Cryo-EM Based Models Space Group Analysis Oligomer Generator Find a Reference Crystal Information Crystal Contacts Visual VIPER FAQs Nucleic Acid Information Lattice Matrices Contact Us Hetero Atoms/Groups Info VIPER Analysis Entries sorted by: Name Index Virus name Virus family T number PDB ID Resolution General Information: diameter, T number, number of subunits, primary citation General Information: T number, number of subunits, primary citation Visualization: capsid topology, subunit fold, quasi-equivalent lattice, subunit organization Visualization: capsid-density rendering, animated map Download files: PDB to VIPER transformation matrix, transformed (VIPER) coordinates Downloadables: CCP4 density map, structure factor file, Derived results: inter-subunit contact tables, inter-subunit association energies, map parameters (header file), VIPER coordinates inter-particle (crystal) contacts, residues at interfaces Figure 1 | Flow chart of the VIPER website organization. The primary data held in VIPER are the atomic coordinates of virus structures obtained by X-ray crystallography. The low–medium-resolution virus structures obtained by cryo-electron microscopy (cryo-EM) and three-dimensional reconstruction techniques are currently being introduced into VIPER. CCP4, collaborative computational project number 4; PDB, Protein Data Bank; T number, triangulation number. the topological features, details of the subunit fold In addition to analysing the existing high-resolution and CAPSOMERES. Crystallization conditions for related crystal structures, VIPER now includes a selected set viruses can be found under the ‘Crystal Information’ of low–medium-resolution virus structures obtained page, which can provide a starting point for the user using cryo-electron microscopy (cryo-EM) techniques. to design crystallization protocols for the new virus. This doubles the number of structures in VIPER and If a study of the assembly/disassembly properties of includes structures of viruses that are too large to this virus is being addressed using mutational analysis crystallize, particles of which the morphology changes and if a reasonable sequence alignment with related at different pH values or ionic strength, structures of viruses exists, then the location of residues suitable intermediates in the pathway of virus assembly, as well for mutation can be determined with the tool ‘Map a as viruses complexed with receptors, antibodies or Residue’. Further, these residues could be analysed for chemically attached proteins BOX 1. their contribution to the stability of specific interfaces VIPER provides a unique opportunity to compare by examining the association-energy calculations pre- virus structures obtained by two independent exper- sented for each of the related structures. If coordinates imental techniques — cryo-EM and crystallography. for the new virus can be obtained by homology mod- While structures obtained by crystallographic meth- elling, using sequence alignment with a closely related ods have details at atomic resolution, there are limi- CAPSOMERES known structure in VIPER, a possible structure for the tations to the size of the virus particles that can be The obvious surface features of whole virus particle can be generated by uploading the studied by this method, and to the homogeneity and the virus particle, which are modelled co ordinates into the ‘OLIGOMER Generator’ amounts of virus samples that are required for crys- observable in an electron- microscopy-reconstructed tool of VIPER. Indeed, structural virologists and tallization. By contrast, recent advances in obtaining density. crystallo graphers can submit the coordinates of newly and analysing cryo-EM data on virus structures has solved virus structures for VIPER analysis through a not only been possible at sub-nanometer resolu- OLIGOMER web-based form that leads to creation of an individual tions, but also provides the necessary information The representation of the protein subunit on the viral web page for the virus, with links to visualizations and to obtain a range of virus structures represented by capsid as dimer, trimer, derived information. A page generated for a user is different populations present in non-homogeneous pentamer, hexamer and so on. accessible only to the user. virus samples. 810 | OCTOBER 2005 | VOLUME 3 www.nature.com/reviews/micro © 2005 Nature Publishing Group REVIEWS Box 1 | Database architecture VIPER was recently upgraded from a static HTML site to a 80 dynamically driven site in which all the pages are created 70 ‘on the fly’ as users browse the site. All of the data presented 60 in VIPER is stored in an underlying relational database using MySQL, which is retrieved and presented using 50 server-side web scripting tools such as PERL (practical 40 extraction and report language), hypertext preprocessor (PHP) and JAVA. The database currently holds 62 unique 30 virus structures — not including the structures of 20 serotypes, mutants and viruses complexed with small ligands — from 21 families and 30 different genera of 10 viruses, all described in the single virus orientation (see
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