Visualizing density maps with UCSF Chimera, Journal of Structural Biology, vol.157, issue.1, pp.281-287, 2007. ,
DOI : 10.1016/j.jsb.2006.06.010
Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes, Journal of Structural Biology, vol.173, issue.3, pp.428-435, 2011. ,
DOI : 10.1016/j.jsb.2010.11.002
2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions, Acta Crystallographica Section D Biological Crystallography, vol.65, issue.7, pp.651-658, 2009. ,
DOI : 10.1107/S0907444909008671
URL : https://hal.archives-ouvertes.fr/in2p3-00016363
Conformational change of proteins arising from normal mode calculations, Protein Engineering Design and Selection, vol.14, issue.1, pp.1-6, 2000. ,
DOI : 10.1093/protein/14.1.1
Coarse-grained normal mode analysis in structural biology, Current Opinion in Structural Biology, vol.15, issue.5, pp.586-592, 2005. ,
DOI : 10.1016/j.sbi.2005.08.007
The design and implementation of an object-oriented toolkit for 3D graphics and visualization, Proceedings of Seventh Annual IEEE Visualization '96, p.93, 1996. ,
DOI : 10.1109/VISUAL.1996.567752
Python and Tkinter programming, 2000. ,
Conception et programmation par objets, Informatique Intelligence Artificielle. InterÉditionsInter´InterÉditions, 1991. ,
??? Programs for Reformatting, Analysis and Manipulation of Biomacromolecular Electron-Density Maps and Reflection Data Sets, Acta Crystallographica Section D Biological Crystallography, vol.52, issue.4, pp.826-828, 1996. ,
DOI : 10.1107/S0907444995014983
Announcing the worldwide Protein Data Bank, Nature Structural Biology, vol.10, issue.12, p.980, 2003. ,
DOI : 10.1038/nsb1203-980
On the computation of structure factors by FFT techniques, Acta Crystallographica Section A Foundations of Crystallography, vol.58, issue.6, pp.568-573, 2002. ,
DOI : 10.1107/S0108767302016318
Efficient structure-factor calculation for large molecules by the fast Fourier transform, Acta Crystallographica Section A, vol.33, issue.3, pp.486-492, 1977. ,
DOI : 10.1107/S0567739477001211
Fast rigid-body refinement for molecular-replacement techniques, Journal of Applied Crystallography, vol.25, issue.2, pp.281-284, 1992. ,
DOI : 10.1107/S0021889891012773
EMDataBank.org: unified data resource for CryoEM, EM- DataBank.org : unified data resource for CryoEM, pp.456-464, 2011. ,
DOI : 10.1093/nar/gkq880
URL : http://doi.org/10.1093/nar/gkv1126
Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs, Microbiology and Molecular Biology Reviews, vol.64, issue.1, 1999. ,
DOI : 10.1128/MMBR.64.1.237-237.2000
The PyMOL Molecular Graphics System, 2002. ,
UCSF Chimera?A visualization system for exploratory research and analysis, Journal of Computational Chemistry, vol.373, issue.13, pp.1605-1612, 2004. ,
DOI : 10.1002/jcc.20084
O : A macromolecule modeling environment Crystallographic and Modeling Methods in Molecular Design, pp.189-199, 1990. ,
Specific Arrangement of ??-Helical Coiled Coils in the Core Domain of the Bacterial Flagellar Hook for the Universal Joint Function, Structure, vol.17, issue.11, pp.1485-1493, 2009. ,
DOI : 10.1016/j.str.2009.08.017
Nucleoprotein-RNA Orientation in the Measles Virus Nucleocapsid by Three-Dimensional Electron Microscopy, Journal of Virology, vol.85, issue.3, pp.1391-1395, 2011. ,
DOI : 10.1128/JVI.01459-10
Architecture of a Dodecameric Bacterial Replicative Helicase, Structure, vol.20, issue.3 ,
DOI : 10.1016/j.str.2012.01.020
URL : https://hal.archives-ouvertes.fr/hal-00965868
Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity, Proceedings of the National Academy of Sciences, vol.107, issue.52, pp.22499-504, 2010. ,
DOI : 10.1073/pnas.1009092107
Two complementary approaches to study peroxisome biogenesis in Saccharomyces cerevisiae: Forward and reversed genetics, Biochimie, vol.75, issue.3-4, pp.209-224, 1993. ,
DOI : 10.1016/0300-9084(93)90079-8
A 200-amino acid ATPase module in search of a basic function, BioEssays, vol.9, issue.7, pp.639-650, 1995. ,
DOI : 10.1002/bies.950170710
AAA+ superfamily ATPases: common structure-diverse function, Genes to Cells, vol.4, issue.7, pp.575-597, 2001. ,
DOI : 10.1101/gad.864401
Evolution and Classification of P-loop Kinases and Related Proteins, Journal of Molecular Biology, vol.333, issue.4, pp.781-815, 2003. ,
DOI : 10.1016/j.jmb.2003.08.040
Classification of AAA+ proteins, Journal of Structural Biology, vol.156, issue.1, pp.2-11, 2006. ,
DOI : 10.1016/j.jsb.2006.05.002
The AAA+ superfamily of functionally diverse proteins, Genome Biology, vol.9, issue.4, p.216, 2008. ,
DOI : 10.1186/gb-2008-9-4-216
AAA+: A class of chaperonelike ATPases associated with the assembly, operation, and disassembly of protein complexes, Genome Res, vol.9, pp.27-43, 1999. ,
Evolutionary history and higher order classification of AAA+ ATPases, Journal of Structural Biology, vol.146, issue.1-2, pp.11-31, 2004. ,
DOI : 10.1016/j.jsb.2003.10.010
Conserved arginine residues implicated in ATP hydrolysis, nucleotide-sensing, and inter-subunit interactions in AAA and AAA+ ATPases, Journal of Structural Biology, vol.146, issue.1-2, pp.106-112, 2004. ,
DOI : 10.1016/j.jsb.2003.11.008
AAA+ proteins: have engine, will work, Nature Reviews Molecular Cell Biology, vol.87, issue.7, pp.519-529, 2005. ,
DOI : 10.1074/jbc.274.37.26225
MoxR AAA+ ATPases: A novel family of molecular chaperones?, Journal of Structural Biology, vol.156, issue.1, pp.200-209, 2006. ,
DOI : 10.1016/j.jsb.2006.02.009
Formation of a Distinctive Complex between the Inducible Bacterial Lysine Decarboxylase and a Novel AAA+ ATPase, Journal of Biological Chemistry, vol.281, issue.3, pp.1532-1546, 2006. ,
DOI : 10.1074/jbc.M511172200
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.12, pp.2256-2268, 2004. ,
DOI : 10.1107/S0907444904026460
Searching protein structure databases with DaliLite v.3, Bioinformatics, vol.24, issue.23, pp.2780-2781, 2008. ,
DOI : 10.1093/bioinformatics/btn507
The structures of HsIU and the ATP-dependent protease HsIU-HsIV, Nature, vol.403, issue.6771, pp.800-805, 2000. ,
DOI : 10.1038/35001629
Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase, Journal of Molecular Biology, vol.311, issue.1, pp.111-122, 2001. ,
DOI : 10.1006/jmbi.2001.4834
A Unique ??-Hairpin Protruding from AAA+ATPase Domain of RuvB Motor Protein Is Involved in the Interaction with RuvA DNA Recognition Protein for Branch Migration of Holliday Junctions, Journal of Biological Chemistry, vol.276, issue.37, pp.35024-35028, 2001. ,
DOI : 10.1074/jbc.M103611200
Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains, Genes & Development, vol.17, issue.20, pp.2552-2563, 2003. ,
DOI : 10.1101/gad.1125603
The roles of the residues on the channel ??-hairpin and loop structures of simian virus 40 hexameric helicase, Proceedings of the National Academy of Sciences, vol.102, issue.32, pp.11248-11253, 2005. ,
DOI : 10.1073/pnas.0409646102
Minichromosome maintenance helicase activity is controlled by N- and C-terminal motifs and requires the ATPase domain helix-2 insert, Proceedings of the National Academy of Sciences, vol.103, issue.20, pp.7613-7618, 2006. ,
DOI : 10.1073/pnas.0509297103
EVOLUTIONARY RELATIONSHIPS AND STRUCTURAL MECHANISMS OF AAA+ PROTEINS, Annual Review of Biophysics and Biomolecular Structure, vol.35, issue.1, pp.93-114, 2006. ,
DOI : 10.1146/annurev.biophys.35.040405.101933
Sequential Peptide Affinity Purification System for the Systematic Isolation and Identification of Protein Complexes from Escherichia coli, Methods Mol Biol, vol.564, pp.373-400, 2009. ,
DOI : 10.1007/978-1-60761-157-8_22
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
The Jpred 3 secondary structure prediction server, Nucleic Acids Research, vol.36, issue.Web Server, pp.197-201, 2008. ,
DOI : 10.1093/nar/gkn238
TopDraw: a sketchpad for protein structure topology cartoons, Bioinformatics, vol.19, issue.2, pp.311-312, 2003. ,
DOI : 10.1093/bioinformatics/19.2.311
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects, Journal of Computational Chemistry, vol.16, issue.1, pp.128-137, 2002. ,
DOI : 10.1002/jcc.1161
Crystal Structure of the Rabies Virus Nucleoprotein-RNA Complex, Science, vol.313, issue.5785, pp.360-363, 2006. ,
DOI : 10.1126/science.1125280
Conformational Flexibility in Recombinant Measles Virus Nucleocapsids Visualised by Cryo-negative Stain Electron Microscopy and Real-space Helical Reconstruction, Journal of Molecular Biology, vol.340, issue.2, pp.319-331, 2004. ,
DOI : 10.1016/j.jmb.2004.05.015
Structural disorder within the replicative complex of measles virus: Functional implications, Virology, vol.344, issue.1, pp.94-110, 2006. ,
DOI : 10.1016/j.virol.2005.09.025
The rule of six, a basic feature for efficient replication of Sendai virus defective interfering RNA, J. Virol, vol.67, pp.4822-4830, 1993. ,
High affinity binding between Hsp70 and the C-terminal domain of the measles virus nucleoprotein requires an Hsp40 co-chaperone, Journal of Molecular Recognition, vol.272, issue.Pt 9, pp.301-315, 2010. ,
DOI : 10.1002/jmr.982
Application of multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins: Structure, Function, and Genetics, vol.6, issue.3, pp.502-511, 2000. ,
DOI : 10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q
The iterative helical real space reconstruction method: Surmounting the problems posed by real polymers, Journal of Structural Biology, vol.157, issue.1, pp.83-94, 2007. ,
DOI : 10.1016/j.jsb.2006.05.015
A robust algorithm for the reconstruction of helical filaments using single-particle methods, Ultramicroscopy, vol.85, issue.4, pp.225-234, 2000. ,
DOI : 10.1016/S0304-3991(00)00062-0
SPIDER and WEB: Processing and Visualization of Images in 3D Electron Microscopy and Related Fields, Journal of Structural Biology, vol.116, issue.1, pp.190-199, 1996. ,
DOI : 10.1006/jsbi.1996.0030
Structure of the Vesicular Stomatitis Virus Nucleoprotein-RNA Complex, Science, vol.313, issue.5785, pp.357-360, 2006. ,
DOI : 10.1126/science.1126953
Computational resources for cryo-electron tomography in Bsoft, Journal of Structural Biology, vol.161, issue.3, pp.232-242, 2008. ,
DOI : 10.1016/j.jsb.2007.08.002
Quantitative Conformational Analysis of Partially Folded Proteins from Residual Dipolar Couplings: Application to the Molecular Recognition Element of Sendai Virus Nucleoprotein, Journal of the American Chemical Society, vol.130, issue.25, pp.8055-8061, 2008. ,
DOI : 10.1021/ja801332d
URL : https://hal.archives-ouvertes.fr/hal-00337329
Characterization of Nucleocapsid Binding by the Measles Virus and Mumps Virus Phosphoproteins, Journal of Virology, vol.78, issue.16, pp.8630-8640, 2004. ,
DOI : 10.1128/JVI.78.16.8630-8640.2004
Measles virus nucleoprotein induces cell-proliferation arrest and apoptosis through NTAIL-NR and NCORE-Fc??RIIB1 interactions, respectively, Journal of General Virology, vol.86, issue.6, pp.1771-1784, 2005. ,
DOI : 10.1099/vir.0.80791-0
Measles Virus (MV) Nucleoprotein Binds to a Novel Cell Surface Receptor Distinct from Fc??RII via Its C-Terminal Domain: Role in MV-Induced Immunosuppression, Journal of Virology, vol.77, issue.21, pp.11332-11346, 2003. ,
DOI : 10.1128/JVI.77.21.11332-11346.2003
The C-terminal Domain of the Measles Virus Nucleoprotein Is Intrinsically Disordered and Folds upon Binding to the C-terminal Moiety of the Phosphoprotein, Journal of Biological Chemistry, vol.278, issue.20, pp.18638-18648, 2003. ,
DOI : 10.1074/jbc.M300518200
EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions, Journal of Structural Biology, vol.128, issue.1, pp.82-97, 1999. ,
DOI : 10.1006/jsbi.1999.4174
Accurate determination of local defocus and specimen tilt in electron microscopy, Journal of Structural Biology, vol.142, issue.3, pp.334-347, 2003. ,
DOI : 10.1016/S1047-8477(03)00069-8
On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation, Acta Crystallographica Section D Biological Crystallography, vol.58, issue.10, pp.1820-1825, 2002. ,
DOI : 10.1107/S0907444902013707
VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs, Journal of Molecular Graphics and Modelling, vol.21, issue.1, pp.47-49, 2002. ,
DOI : 10.1016/S1093-3263(02)00123-7
The 12?? Structure of Trypsin-treated Measles Virus N???RNA, Journal of Molecular Biology, vol.339, issue.2, pp.301-312, 2004. ,
DOI : 10.1016/j.jmb.2004.03.073
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs, Nature Protocols, vol.6, issue.12, pp.1941-1974, 2008. ,
DOI : 10.1006/jsbi.1997.3845
Rescue of Synthetic Measles Virus Minireplicons: Measles Genomic Termini Direct Efficient Expression and Propagation of a Reporter Gene, Virology, vol.208, issue.2, pp.800-807, 1995. ,
DOI : 10.1006/viro.1995.1215
Crystal Structure of a Nucleocapsid-Like Nucleoprotein-RNA Complex of Respiratory Syncytial Virus, Science, vol.326, issue.5957, pp.1279-1283, 2009. ,
DOI : 10.1126/science.1177634
URL : https://hal.archives-ouvertes.fr/pasteur-00457523
A New Generation of the IMAGIC Image Processing System, Journal of Structural Biology, vol.116, issue.1, pp.17-24, 1996. ,
DOI : 10.1006/jsbi.1996.0004
Hsp72 recognizes a P binding motif in the measles virus N protein C-terminus, Virology, vol.337, issue.1, pp.162-174, 2005. ,
DOI : 10.1016/j.virol.2005.03.035
Cependant, cette technique estparticulì erement difficilè a mettre en oeuvre dans le cas de complexes de taille importante La microscopié electronique permet, elle, de visualiser des particules de grande taille dans des conditions proches de celles in vivo. Cependant, la résolution des reconstructions tridimensionnelles obtenues exclut, en général, leur interprétation directe en termes de structures moléculaires, ´ etape nécessairè a la compréhension desprobì emes biologiques. Il est donc naturel d'essayer de combiner les informations fournies par ces deux techniques pour caractériser la structure des assemblages macromoléculaires. L'idée est de positionner les modèles moléculaires déterminés par cristallographiè a l'intérieur de reconstructions 3D issues de la microscopié electronique, et de comparer la densitédensitéélectronique associéè a la reconstruction 3D avec une densitédensitéélectronique calculéè a partir des modèles, de macromolécules produit couramment des modèles moléculairesmoléculairesà résolution atomique ,
nommé ???? est un environnement graphique convivial, intégrant la possibilité de recalage flexible, et un moteur de calcul performant (calcul rapide, traitement de symétries complexes, utilisation de grands volumes Testé sur des dizaines de cas réels, ???? est aujourd'hui pleinement fonctionnel et est utilisé par un nombre croissant de chercheurs, en France etàetà l'´ etranger ,