C. Cianci, . Ct, N. Meanwell, H. Putz, M. Hagen et al., Identification of N-Hydroxamic Acid and N-Hydroxyimide Compounds that Inhibit the Influenza Virus Polymerase, Antiviral Chemistry and Chemotherapy, vol.171, issue.6, pp.353-360, 1996.
DOI : 10.1177/095632029600700609

T. Crepin, A. Dias, S. Cusack, R. Ruigrok, A. Palencia et al., Mutational and Metal Binding Analysis of the Endonuclease Domain of the Influenza Virus Polymerase PA Subunit, Journal of Virology, vol.84, issue.18, 2010.
DOI : 10.1128/JVI.00995-10

K. Das, J. Aramini, L. Ma, and R. Krug, Structures of influenza A proteins and insights into antiviral drug targets, Nature Structural & Molecular Biology, vol.68, issue.5, pp.530-538
DOI : 10.1529/biophysj.106.090183

A. Dias, D. Bouvier, T. Crepin, A. Mccarthy, D. Hart et al., The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit, Nature, vol.13, issue.7240, pp.914-918, 2009.
DOI : 10.1038/nature07745

L. Doan, B. Handa, N. Roberts, and K. Klumpp, Metal Ion Catalysis of RNA Cleavage by the Influenza Virus Endonuclease, Biochemistry, vol.38, issue.17, pp.5612-5619, 1999.
DOI : 10.1021/bi9828932

U. Ericsson, B. Hallberg, G. Detitta, N. Dekker, and P. Nordlund, Thermofluor-based high-throughput stability optimization of proteins for structural studies, Analytical Biochemistry, vol.357, issue.2, pp.289-298, 2006.
DOI : 10.1016/j.ab.2006.07.027

R. Esnouf, version 1.4, including reading and contouring of electron-density maps, Acta Crystallographica Section D Biological Crystallography, vol.55, issue.4, pp.938-940, 1999.
DOI : 10.1107/S0907444998017363

J. Gong, H. Fang, M. Li, Y. Liu, K. Yang et al., Potential Targets and Their Relevant Inhibitors in Anti-influenza Fields, Current Medicinal Chemistry, vol.16, issue.28, 2009.
DOI : 10.2174/092986709789104984

P. Gouet, E. Courcelle, D. Stuart, and F. Metoz, ESPript: analysis of multiple sequence alignments in PostScript, Bioinformatics, vol.15, issue.4, pp.305-308, 1999.
DOI : 10.1093/bioinformatics/15.4.305
URL : https://hal.archives-ouvertes.fr/hal-00314288

D. Guilligay, F. Tarendeau, P. Resa-infante, R. Coloma, T. Crepin et al., The structural basis for cap binding by influenza virus polymerase subunit PB2, Nature Structural & Molecular Biology, vol.70, issue.5, pp.500-506, 2008.
DOI : 10.1002/prot.10286

S. Hare, S. Gupta, E. Valkov, A. Engelman, and P. Cherepanov, Retroviral intasome assembly and inhibition of DNA strand transfer, Nature, vol.25, issue.7286, pp.232-236
DOI : 10.1038/nature08784

J. Hastings, H. Selnick, B. Wolanski, and J. Tomassini, Anti-influenza virus activities of 4- substituted 2,4-dioxobutanoic acid inhibitors, Antimicrobial agents and chemotherapy, vol.40, issue.5, pp.1304-1307, 1996.

Y. Iwai, H. Takahashi, D. Hatakeyama, K. Motoshima, M. Ishikawa et al., Anti-influenza activity of phenethylphenylphthalimide analogs derived from thalidomide, Bioorganic & Medicinal Chemistry, vol.18, issue.14, pp.5379-5390
DOI : 10.1016/j.bmc.2010.05.035

W. Kabsch, Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants, Journal of Applied Crystallography, vol.26, issue.6, pp.795-800, 1993.
DOI : 10.1107/S0021889893005588

P. Kraulis, MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, Journal of Applied Crystallography, vol.24, issue.5, pp.946-950, 1991.
DOI : 10.1107/S0021889891004399

R. Krug and J. Aramini, Emerging antiviral targets for influenza A virus, Trends in Pharmacological Sciences, vol.30, issue.6, pp.269-277, 2009.
DOI : 10.1016/j.tips.2009.03.002

T. Kuzuhara, Y. Iwai, H. Takahashi, D. Hatakeyama, and N. Echigo, Green tea catechins inhibit the endonuclease activity of influenza A virus RNA polymerase, PLoS Currents, vol.1, p.1052, 2009.
DOI : 10.1371/currents.RRN1052

E. Merritt and D. Bacon, [26] Raster3D: Photorealistic molecular graphics, Methods in enzymology, vol.277, pp.505-524, 1997.
DOI : 10.1016/S0076-6879(97)77028-9

G. Murshudov, Refinement of Macromolecular Structures by the Maximum-Likelihood Method, Acta Crystallographica Section D Biological Crystallography, vol.53, issue.3, pp.240-255, 1997.
DOI : 10.1107/S0907444996012255

M. Nakazawa, S. Kadowaki, I. Watanabe, Y. Kadowaki, M. Takei et al., PA subunit of RNA polymerase as a promising target for anti-influenza virus agents, Antiviral Research, vol.78, issue.3, pp.194-201, 2008.
DOI : 10.1016/j.antiviral.2007.12.010

K. Parkes, P. Ermert, J. Fassler, J. Ives, J. Martin et al., Use of a Pharmacophore Model To Discover a New Class of Influenza Endonuclease Inhibitors, Journal of Medicinal Chemistry, vol.46, issue.7, pp.1153-1164, 2003.
DOI : 10.1021/jm020334u

S. Plotch, M. Bouloy, I. Ulmanen, and R. Krug, A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription, Cell, vol.23, issue.3, pp.847-858, 1981.
DOI : 10.1016/0092-8674(81)90449-9

L. Poon, D. Pritlove, E. Fodor, and G. Brownlee, Direct evidence that the poly(A) tail of influenza A virus mRNA is synthesized by reiterative copying of a U track in the virion RNA template, Journal of virology, vol.73, issue.4, pp.3473-3476, 1999.

R. Read, Pushing the boundaries of molecular replacement with maximum likelihood, Acta crystallographica, vol.57, pp.1373-1382, 2001.

J. Reguera, F. Weber, and S. Cusack, Bunyaviridae RNA polymerases (L-protein) have an Nterminal , influenza-like endonuclease domain, essential for viral cap-dependent transcription, PLoS pathogens, vol.6, issue.9, 2010.

R. Ruigrok, T. Crepin, D. Hart, and S. Cusack, Towards an atomic resolution understanding of the influenza virus replication machinery, Current Opinion in Structural Biology, vol.20, issue.1, pp.104-113, 2010.
DOI : 10.1016/j.sbi.2009.12.007

V. Summa, A. Petrocchi, F. Bonelli, B. Crescenzi, M. Donghi et al., Discovery of Raltegravir, a Potent, Selective Orally Bioavailable HIV-Integrase Inhibitor for the Treatment of HIV-AIDS Infection, Journal of Medicinal Chemistry, vol.51, issue.18, pp.5843-5855, 2008.
DOI : 10.1021/jm800245z

J. Tomassini, H. Selnick, M. Davies, M. Armstrong, J. Baldwin et al., Inhibition of cap (m7GpppXm)-dependent endonuclease of influenza virus by 4-substituted 2,4-dioxobutanoic acid compounds., Antimicrobial Agents and Chemotherapy, vol.38, issue.12, pp.2827-2837, 1994.
DOI : 10.1128/AAC.38.12.2827

J. Tomassini, M. Davies, J. Hastings, R. Lingham, M. Mojena et al., A novel antiviral agent which inhibits the endonuclease of influenza viruses, Antimicrobial agents and chemotherapy, vol.40, issue.5, pp.1189-1193, 1996.

P. Yuan, M. Bartlam, Z. Lou, S. Chen, J. Zhou et al., Crystal structure of an avian influenza polymerase PAN reveals an endonuclease active site, Nature, vol.54, issue.7240, pp.909-913, 2009.
DOI : 10.1038/nature07720

A. Ablasser, F. Bauernfeind, G. Hartmann, E. Latz, K. Fitzgerald et al., RIG-Idependent sensing of poly(dA:dT) through the induction of an RNA polymerase IIItranscribed RNA intermediate, Nat Immunol, 2009.

J. Andrejeva, K. Childs, D. Young, T. Carlos, N. Stock et al., The V proteins of paramyxoviruses bind the IFN-inducible RNA helicase, mda-5, and inhibit its activation of the IFN-beta promoter, Proc Natl Acad Sci, 2004.

C. Arias, M. Escalera-zamudio, L. Soto-del-río-mde, A. Cobián-güemes, P. Isa et al., Molecular Anatomy of 2009 Influenza Virus A (H1N1), Archives of Medical Research, vol.40, issue.8, 2009.
DOI : 10.1016/j.arcmed.2009.10.007

K. Arimoto, H. Takahashi, T. Hishiki, H. Konishi, T. Fujita et al., Negative regulation of the RIG-I signaling by the ubiquitin ligase RNF125, Proceedings of the National Academy of Sciences, vol.104, issue.18, 2007.
DOI : 10.1073/pnas.0611551104

R. Ash, Influenza: The State of Our Ignorance. Science, 2006.

X. Bao, D. Kolli, T. Liu, Y. Shan, R. Garofalo et al., Human metapneumovirus small hydrophobic protein inhibits NF-kappaB transcriptional activity, J Virol, 2008.

M. Barber, J. Aldridge, . Jr, R. Webster, and K. Magor, Association of RIG-I with innate immunity of ducks to influenza, Proceedings of the National Academy of Sciences, vol.107, issue.13, 2010.
DOI : 10.1073/pnas.1001755107

M. Baril, M. Racine, F. Penin, and D. Lamarre, MAVS Dimer Is a Crucial Signaling Component of Innate Immunity and the Target of Hepatitis C Virus NS3/4A Protease, Journal of Virology, vol.83, issue.3, 2009.
DOI : 10.1128/JVI.01659-08

M. Bartlam, Z. Lou, Y. Liu, and Z. Rao, Polymerase structure and funciton, Influenza molecular virology. Wang Q and Tao YJ, 2010.

A. Baum, R. Sachidanandam, and A. García-sastre, Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing, Proceedings of the National Academy of Sciences, vol.107, issue.37, 2010.
DOI : 10.1073/pnas.1005077107

B. Beutler, Microbe sensing, positive feedback loops, and the pathogenesis of inflammatory diseases, Immunological Reviews, vol.439, issue.1, 2009.
DOI : 10.1111/j.1600-065X.2008.00733.x

L. Bouchier-hayes and S. Martin, CARD games in apoptosis and immunity, EMBO Reports, vol.3, issue.7, 20023.
DOI : 10.1093/embo-reports/kvf139

N. Bouvier and P. Palese, The biology of influenza viruses. Vaccine, 2008.

A. Brünger, Assessment of phase accuracy by cross validation: the free R value. Methods and applications, Acta Crystallographica Section D Biological Crystallography, vol.49, issue.1, 1993.
DOI : 10.1107/S0907444992007352

X. Cao, New DNA-sensing pathway feeds RIG-I with RNA, Nature Immunology, vol.25, issue.10, 2009.
DOI : 10.1038/ni1009-1049

C. Cazenave and O. Uhlenbeck, RNA template-directed RNA synthesis by T7 RNA polymerase., Proceedings of the National Academy of Sciences, vol.91, issue.15, 1994.
DOI : 10.1073/pnas.91.15.6972

V. Chen, J. Headd, D. Keedy, R. Immormino, G. Kapral et al., MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr D Biol Crystallogr, 2010.

Y. Chen and A. Clark, Equilibrium and Kinetic Folding of a ??-Helical Greek Key Protein Domain:?? Caspase Recruitment Domain (CARD) of RICK, Biochemistry, vol.42, issue.20, p.42, 2003.
DOI : 10.1021/bi0340752

Y. Chen and A. Clark, Kinetic traps in the folding/unfolding of procaspase-1 CARD domain, Protein Science, vol.268, issue.8, 2004.
DOI : 10.1110/ps.03521504

K. Childs, N. Stock, C. Ross, J. Andrejeva, L. Hilton et al., Mda-5, but not RIG-I, is a common target for paramyxovirus V proteins. Virology, 2007.

K. Childs, J. Andrejeva, R. Randall, and S. Goodbourn, Mechanism of mda-5 Inhibition by Paramyxovirus V Proteins, Journal of Virology, vol.83, issue.3, 2009.
DOI : 10.1128/JVI.01768-08

Y. Chiu, J. Macmillan, and Z. Chen, RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway. Cell, 2009.

O. Cordin, J. Banroques, N. Tanner, and P. Linder, The DEAD-box protein family of RNA helicases, Gene, vol.367, pp.17-37, 2006.
DOI : 10.1016/j.gene.2005.10.019
URL : https://hal.archives-ouvertes.fr/hal-00132162

N. Coussens, J. Mowers, C. Mcdonald, G. Nunez, and S. Ramaswamy, Crystal structure of the Nod1 caspase activation and recruitment domain, Biochemical and Biophysical Research Communications, vol.353, issue.1, 2007.
DOI : 10.1016/j.bbrc.2006.11.122

C. Cronin, K. Lim, and R. J. , Production of selenomethionyl-derivatized proteins in baculovirus-infected insect cells, Protein Science, vol.58, issue.9, 2007.
DOI : 10.1110/ps.072931407

S. Cui, K. Eisenächer, A. Kirchhofer, K. Brzózka, A. Lammens et al., The C-terminal regulatory domain is the RNA 5'-triphosphate sensor of RIG-I. Mol Cell, 2008.

D. , P. Amenta, J. Reiss, and C. , IFN-beta-induced alteration of VSV protein phosphorylation in neuronal cells, Viral Immunol, 2009.

K. Das, J. Aramini, L. Ma, R. Krug, and E. Arnold, Structures of influenza A proteins and insights into antiviral drug targets, Nature Structural & Molecular Biology, vol.68, issue.5, 2010.
DOI : 10.1529/biophysj.106.090183

D. Falco, F. Cainarca, S. Andolfi, G. Ferrentino, R. Berti et al., X-linked Opitz syndrome: novel mutations in the MID1 gene and redefinition of the clinical spectrum, Am J Med Genet A, 2003.

E. De-la-fortelle and G. Bricogne, [27] Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods, Methods in Enzymology, p.276, 1997.
DOI : 10.1016/S0076-6879(97)76073-7

L. Deng, P. Dai, T. Parikh, H. Cao, V. Bhoj et al., Vaccinia virus subverts a MAVS-dependent innate immune response in keratinocytes through its dsRNA binding protein E3, J Virol, 2008.

J. Desmyter, J. Melnick, and W. Rawls, Defectiveness of interferon production and of rubella virus interference in a line of African green monkey kidney cells (Vero), J Virol, 1968.

A. Dias, D. Bouvier, T. Crépin, A. Mccarthy, D. Hart et al., The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit, Nature, vol.13, issue.7240, 2009.
DOI : 10.1038/nature07745

E. Dixit, S. Boulant, Y. Zhang, A. Lee, C. Odendall et al., Peroxisomes Are Signaling Platforms for Antiviral Innate Immunity, Cell, vol.141, issue.4, 2010.
DOI : 10.1016/j.cell.2010.04.018

P. Emsley and K. Cowtan, : model-building tools for molecular graphics, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.12, 2004.
DOI : 10.1107/S0907444904019158

U. Ericsson, B. Hallberg, G. Detitta, N. Dekker, and P. Nordlund, Thermofluor-based highthroughput stability optimization of proteins for structural studies, Anal Biochem, 2006.

L. Fan, T. Briese, and W. Lipkin, Z Proteins of New World Arenaviruses Bind RIG-I and Interfere with Type I Interferon Induction, Journal of Virology, vol.84, issue.4, 2010.
DOI : 10.1128/JVI.01362-09

D. Fitzgerald, P. Berger, C. Schaffitzel, K. Yamada, T. Richmond et al., Protein complex expression by using multigene baculoviral vectors. Nat Methods, 2006.

M. J. Forstner, . Appl, and . Cryst, SAXS, SANS and X-ray crystallography as complementary methods in the study of biological form and function, Journal of Applied Crystallography, vol.33, issue.3, pp.519-523, 2000.
DOI : 10.1107/S0021889899014363

C. Friedman, O. Donnell, M. Legarda-addison, D. Ng, A. Cárdenas et al., The tumour suppressor CYLD is a negative regulator of RIG-I-mediated antiviral response, EMBO reports, vol.175, issue.9, 2008.
DOI : 10.1038/ni1465

T. Fujita, A Nonself RNA Pattern: Tri-p to Panhandle, Immunity, vol.31, issue.1, 2009.
DOI : 10.1016/j.immuni.2009.06.014

M. Gack, Y. Shin, C. Joo, T. Urano, C. Liang et al., TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity, Nature, vol.7, issue.7138, 2007.
DOI : 10.1038/nature05732

M. Gack, R. Albrecht, T. Urano, K. Inn, I. Huang et al., Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Cell Host Microbe, 2009.

M. Gack, A. Kirchhofer, Y. Shin, K. Inn, C. Liang et al., Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated antiviral signal transduction, Proceedings of the National Academy of Sciences, vol.105, issue.43, 2008.
DOI : 10.1073/pnas.0804947105

M. Gack, E. Nistal-villán, K. Inn, A. García-sastre, and J. Jung, Phosphorylation-Mediated Negative Regulation of RIG-I Antiviral Activity, Journal of Virology, vol.84, issue.7, 2010.
DOI : 10.1128/JVI.02241-09

D. Gao, Y. Yang, R. Wang, X. Zhou, F. Diao et al., REUL is a novel E3 ubiquitin ligase and stimulator of retinoic-acid-inducible gene-I. PLoS One, 2009.

L. Gitlin, W. Barchet, S. Gilfillan, M. Cella, B. Beutler et al., Essential role of mda-5 in type I IFN responses to polyriboinosinic:polyribocytidylic acid and encephalomyocarditis picornavirus, Proceedings of the National Academy of Sciences, vol.103, issue.22, 2006.
DOI : 10.1073/pnas.0603082103

C. Grütter, C. Briand, G. Capitani, P. Mittl, S. Papin et al., Structure of the PRYSPRY-domain: Implications for autoinflammatory diseases, FEBS Letters, vol.17, issue.1, 2006.
DOI : 10.1016/j.febslet.2005.11.076

P. Gouet, E. Courcelle, D. Stuart, and F. Métoz, ESPript: analysis of multiple sequence alignments in PostScript, Bioinformatics, vol.15, issue.4, 1999.
DOI : 10.1093/bioinformatics/15.4.305
URL : https://hal.archives-ouvertes.fr/hal-00314288

Z. Guo, L. Chen, H. Zeng, J. Gomez, J. Plowden et al., NS1 Protein of Influenza A Virus Inhibits the Function of Intracytoplasmic Pathogen Sensor, RIG-I, American Journal of Respiratory Cell and Molecular Biology, vol.36, issue.3, 2007.
DOI : 10.1165/rcmb.2006-0283RC

M. Habjan, I. Andersson, J. Klingström, M. Schümann, A. Martin et al., Processing of Genome 5??? Termini as a Strategy of Negative-Strand RNA Viruses to Avoid RIG-I-Dependent Interferon Induction, PLoS ONE, vol.70, issue.10, 2008.
DOI : 10.1371/journal.pone.0002032.t001

S. Hausmann, J. Marq, C. Tapparel, D. Kolakofsky, and D. Garcin, RIG-I and dsRNA-Induced IFN?? Activation, PLoS ONE, vol.63, issue.12, p.3965, 2008.
DOI : 10.1371/journal.pone.0003965.g008
URL : http://doi.org/10.1371/journal.pone.0003965

M. Hilbert, A. Karow, and D. Klostermeier, The mechanism of ATP-dependent RNA unwinding by DEAD box proteins, Biological Chemistry, vol.390, issue.12, 2009.
DOI : 10.1515/BC.2009.135

L. Holm and P. Rosenström, Dali server: conservation mapping in 3D, Nucleic Acids Research, vol.38, issue.Web Server, pp.545-549, 2010.
DOI : 10.1093/nar/gkq366
URL : http://doi.org/10.1093/nar/gkq366

V. Hornung, A. Ablasser, M. Charrel-dennis, F. Bauernfeind, G. Horvath et al., AIM2 recognizes cytosolic dsDNA and forms a caspase-1-activating inflammasome with ASC, Nature, vol.326, issue.7237, 2009.
DOI : 10.1038/nature07725

V. Hornung, J. Ellegast, S. Kim, K. Brzozka, A. Jung et al., 5'-Triphosphate RNA is the ligand for RIG-I. Science, 2006.

H. Ishikawa and G. Barber, STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling, Nature, 2008.

L. James, A. Keeble, Z. Khan, D. Rhodes, and J. Trowsdale, Structural basis for PRYSPRYmediated tripartite motif (TRIM) protein function, Proc Natl Acad Sci, 2007.

E. Jankowsky and M. Fairman, RNA helicases ??? one fold for many functions, Current Opinion in Structural Biology, vol.17, issue.3, 2007.
DOI : 10.1016/j.sbi.2007.05.007

E. Jankowsky and A. Putnam, Duplex Unwinding with DEAD-Box Proteins, Methods Mol Biol, 2010.
DOI : 10.1007/978-1-60327-355-8_18

H. Kato, O. Takeuchi, E. Mikamo-satoh, R. Hirai, T. Kawai et al., Length-dependent recognition of double-stranded ribonucleic acids by retinoic acid???inducible gene-I and melanoma differentiation???associated gene 5, The Journal of Experimental Medicine, vol.89, issue.7, 2008.
DOI : 10.1016/j.jsb.2005.05.002

H. Kato, O. Takeuchi, S. Sato, M. Yoneyama, M. Yamamoto et al., Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses, Nature, vol.78, issue.7089, 2006.
DOI : 10.1038/nature04734

T. Kawai and S. Akira, Antiviral Signaling Through Pattern Recognition Receptors, Journal of Biochemistry, vol.141, issue.2, 2007.
DOI : 10.1093/jb/mvm032
URL : http://jb.oxfordjournals.org/cgi/content/short/141/2/137

T. Kawai and S. Akira, SnapShot: Pattern-Recognition Receptors, Cell, vol.129, issue.5, 2007.
DOI : 10.1016/j.cell.2007.05.017

T. Kawai, K. Takahashi, S. Sato, C. Coban, H. Kumar et al., IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction, Nature Immunology, vol.174, issue.10, 2005.
DOI : 10.1093/emboj/cdf505

A. Keeble, Z. Khan, A. Forster, and L. James, TRIM21 is an IgG receptor that is structurally, thermodynamically, and kinetically conserved, Proceedings of the National Academy of Sciences, vol.105, issue.16, 2008.
DOI : 10.1073/pnas.0800159105

N. Kholod, K. Vassilenko, M. Shlyapnikov, V. Ksenzenko, and L. Kisselev, Preparation of active tRNA gene transcripts devoid of 3'-extended products and dimers, Nucleic Acids Research, vol.26, issue.10, 1998.
DOI : 10.1093/nar/26.10.2500

D. Komander, F. Reyes-turcu, J. Licchesi, P. Odenwaelder, K. Wilkinson et al., Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains, 2009.

G. Langer, S. Cohen, A. Perrakis, and V. Lamzin, Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7, Nature Protocols, vol.60, issue.7, 2008.
DOI : 10.1038/nprot.2008.91

M. Larkin, G. Blackshields, N. Brown, R. Chenna, P. Mcgettigan et al., ClustalW and ClustalX version 2, Bioinformatics, issue.21, p.23, 2007.

A. G. Leslie, Recent changes to the MOSFLM package for processing film and image plate data Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography, 1992.

T. Li, X. Chen, K. Garbutt, P. Zhou, and N. Zheng, Structure of DDB1 in Complex with a Paramyxovirus V Protein: Viral Hijack of a Propeller Cluster in Ubiquitin Ligase, Cell, vol.124, issue.1, 2006.
DOI : 10.1016/j.cell.2005.10.033

X. Li, C. Lu, M. Stewart, H. Xu, R. Strong et al., Structural basis of doublestranded RNA recognition by the RIG-I like receptor MDA5, Arch Biochem Biophys, 2009.

X. Li, C. Ranjith-kumar, M. Brooks, S. Dharmaiah, A. Herr et al., The RIG-I-like Receptor LGP2 Recognizes the Termini of Double-stranded RNA, Journal of Biological Chemistry, vol.284, issue.20, 2009.
DOI : 10.1074/jbc.M900818200

X. Li, L. Sun, R. Seth, G. Pineda, and Z. Chen, Hepatitis C virus protease NS3/4A cleaves mitochondrial antiviral signaling protein off the mitochondria to evade innate immunity, Proceedings of the National Academy of Sciences, vol.102, issue.49, 2005.
DOI : 10.1073/pnas.0508531102

S. Lin, Y. Lo, and H. Wu, Helical assembly in the MyD88???IRAK4???IRAK2 complex in TLR/IL-1R signalling, Nature, vol.25, issue.7300, 2010.
DOI : 10.1038/nature09121

P. Lindner, Quick Guide: DEAD-box proteins, Curr Biol, p.10, 2000.

Z. Ling, K. Tran, M. J. Teng, and . Virol, Human Respiratory Syncytial Virus Nonstructural Protein NS2 Antagonizes the Activation of Beta Interferon Transcription by Interacting with RIG-I, Journal of Virology, vol.83, issue.8, 2009.
DOI : 10.1128/JVI.02434-08

C. Lu, H. Xu, C. Ranjith-kumar, M. Brooks, T. Hou et al., The Structural Basis of 5??? Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain, Structure, vol.18, issue.8, 2010.
DOI : 10.1016/j.str.2010.05.007

F. Manon, A. Favier, G. Nunez, J. Simorre, and S. Cusack, Solution Structure of NOD1 CARD and Mutational Analysis of its Interaction with the CARD of Downstream Kinase RICK, Journal of Molecular Biology, vol.365, issue.1, 2007.
DOI : 10.1016/j.jmb.2006.09.067

F. Martinon and J. Tschopp, Inflammatory Caspases, Cell, vol.117, issue.5, 2004.
DOI : 10.1016/j.cell.2004.05.004
URL : http://doi.org/10.1016/j.cell.2004.05.004

E. Meylan, J. Curran, K. Hofmann, D. Moradpour, M. Binder et al., Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus, Nature, vol.69, issue.7062, 2005.
DOI : 10.1016/j.cell.2005.08.012

S. Milam, N. Nicely, B. Feeney, C. Mattos, and A. Clark, Rapid Folding and Unfolding of Apaf-1 CARD, Journal of Molecular Biology, vol.369, issue.1, 2007.
DOI : 10.1016/j.jmb.2007.02.105

J. Milligan and O. Uhlenbeck, [5] Synthesis of small RNAs using T7 RNA polymerase, Methods Enzymol, 1989.
DOI : 10.1016/0076-6879(89)80091-6

H. Moon and J. Choe, Crystallization and preliminary crystallographic studies of human RIG-I in complex with double-stranded RNA, Acta Crystallographica Section F Structural Biology and Crystallization Communications, vol.65, issue.6, 2009.
DOI : 10.1107/S1744309109018405

C. Moore, D. Bergstralh, J. Duncan, Y. Lei, T. Morrison et al., NLRX1 is a regulator of mitochondrial antiviral immunity, Nature, vol.104, issue.7178, 2008.
DOI : 10.1038/nature06501

A. Murali, X. Li, C. Ranjith-kumar, K. Bhardwaj, A. Holzenburg et al., Structure and Function of LGP2, a DEX(D/H) Helicase That Regulates the Innate Immunity Response, Journal of Biological Chemistry, vol.283, issue.23, 2008.
DOI : 10.1074/jbc.M800542200

S. Myong, S. Cui, P. Cornish, A. Kirchhofer, M. Gack et al., Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA. Science, 2009.

T. Nishino, K. Komori, D. Tsuchiya, Y. Ishino, and K. Morikawa, Crystal Structure and Functional Implications of Pyrococcus furiosus Hef Helicase Domain Involved in Branched DNA Processing, Structure, vol.13, issue.1, 2005.
DOI : 10.1016/j.str.2004.11.008

S. Nisole, J. Stoye, and A. Saib, TRIM family proteins: retroviral restriction and antiviral defence, Nature Reviews Microbiology, vol.3, issue.10, 2005.
DOI : 10.1128/JVI.75.13.6204-6208.2001

E. Nistal-villan, M. Gack, G. Martínez-delgado, N. Maharaj, K. Inn et al., Negative role of RIG-I serine 8 phosphorylation in the regulation of interferon-beta production, J Biol Chem, 2010.

J. Marq, D. Kolakofsky, and D. Garcin, Unpaired 5' ppp-nucleotides, as found in arenavirus double-stranded RNA panhandles, are not recognized by RIG-I, J Biol Chem, 2010.

B. Matthews, Solvent content of protein crystals, Journal of Molecular Biology, vol.33, issue.2, 1968.
DOI : 10.1016/0022-2836(68)90205-2

S. Minucci, M. Maccarana, M. Cioce, D. Luca, P. Gelmetti et al., Oligomerization of RAR and AML1 Transcription Factors as a Novel Mechanism of Oncogenic Activation, Molecular Cell, vol.5, issue.5, 2000.
DOI : 10.1016/S1097-2765(00)80321-4

T. Monie, M. Moncrieffe, and N. Gay, Structure and regulation of cytoplasmic adapter proteins involved in innate immune signaling, Immunological Reviews, vol.30, issue.1, 2009.
DOI : 10.1111/j.1600-065X.2008.00735.x

H. Oshiumi, M. Matsumoto, S. Hatakeyama, and T. Seya, Riplet/RNF135, a RING finger protein, ubiquitinates RIG-I to promote interferon-beta induction during the early phase of viral infection, J Biol Chem, 2009.

K. Ozato, D. Shin, T. Chang, and H. Morse, TRIM family proteins and their emerging roles in innate immunity, Nature Reviews Immunology, vol.361, issue.11, 2008.
DOI : 10.1038/nri2413

M. Pantoliano, E. Petrella, J. Kwasnoski, V. Lobanov, J. Myslik et al., High-Density Miniaturized Thermal Shift Assays as a General Strategy for Drug Discovery, Journal of Biomolecular Screening, vol.6, issue.6, 2001.
DOI : 10.1177/108705710100600609

P. Palese and M. Shaw, Orthomzxoviridae: the viruses and their replication, Fields virologzy. Philadelphia:Lippincott Williams and Wilkins, 2007.

J. Parisien, D. Bamming, A. Komuro, A. Ramachandran, J. Rodriguez et al., A Shared Interface Mediates Paramyxovirus Interference with Antiviral RNA Helicases MDA5 and LGP2, Journal of Virology, vol.83, issue.14, 2009.
DOI : 10.1128/JVI.00153-09

A. Pichlmair, O. Schulz, C. Tan, T. Naslund, P. Liljestrom et al., RIG-Imediated antiviral responses to single-stranded RNA bearing 5'-phosphates. Science, 2006.
DOI : 10.1126/science.1132998

C. Pickart and D. Fushman, Polyubiquitin chains: polymeric protein signals, Current Opinion in Chemical Biology, vol.8, issue.6, 2004.
DOI : 10.1016/j.cbpa.2004.09.009

D. Pippig, J. Hellmuth, S. Cui, A. Kirchhofer, K. Lammens et al., The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA, Nucleic Acids Research, vol.37, issue.6, 2009.
DOI : 10.1093/nar/gkp059

S. Plumet, F. Herschke, J. Bourhis, H. Valentin, S. Longhi et al., Cytosolic 5'- triphosphate ended viral leader transcript of measles virus as activator of the RIG Imediated interferon response. PLoS ONE, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00175648

E. Poole, B. He, R. Lamb, R. Randall, and S. Goodbourn, The V proteins of simian virus 5 and other paramyxoviruses inhibit induction of interferon-beta. Virology, 2002.

J. Potter, R. Randall, and G. Taylor, Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain, BMC Structural Biology, vol.8, issue.1, 2008.
DOI : 10.1186/1472-6807-8-11

. Pymol, DeLano Scientific LLC, 400 Oyster Point Blvd, Suite 213 South, pp.94080-1918

H. Qin, S. Srinivasula, G. Wu, T. Fernandes-alnemri, E. Alnemri et al., Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1, Nature, 1999.

C. Ranjith-kumar, A. Murali, W. Dong, D. Srisathiyanarayanan, R. Vaughan et al., Agonist and Antagonist Recognition by RIG-I, a Cytoplasmic Innate Immunity Receptor, Journal of Biological Chemistry, vol.284, issue.2, 2009.
DOI : 10.1074/jbc.M806219200

R. Read, Pushing the boundaries of molecular replacement with maximum likelihood, Acta Crystallogr D Biol Crystallogr Oct. Erratum Acta Crystallogr D Biol Crystallogr Feb, 2001.

A. Reymond, G. Meroni, A. Fantozzi, G. Merla, S. Cairo et al., The tripartite motif family identifies cell compartments, The EMBO Journal, vol.20, issue.9, 2001.
DOI : 10.1093/emboj/20.9.2140

D. Rhodes, B. De-bono, and J. Trowsdale, Relationship between SPRY and B30.2 protein domains . Evolution of a component of immune defence? Immunology, 2005.

M. Rossmann, The molecular replacement method, Acta Crystallographica Section A Foundations of Crystallography, vol.46, issue.2, 1990.
DOI : 10.1107/S0108767389009815

J. Rehwinkel, C. Tan, D. Goubau, O. Schulz, A. Pichlmair et al., RIG-I Detects Viral Genomic RNA during Negative-Strand RNA Virus Infection, Cell, vol.140, issue.3, 2010.
DOI : 10.1016/j.cell.2010.01.020
URL : http://doi.org/10.1016/j.cell.2010.01.020

G. Salvesen and S. Riedl, Structure of the Fas/FADD complex: A conditional death domain complex mediating signaling by receptor clustering, Cell Cycle, vol.8, issue.17, 2009.
DOI : 10.4161/cc.8.17.9399

T. Saito, R. Hirai, Y. Loo, D. Owen, C. Johnson et al., Regulation of innate antiviral defenses through a shared repressor domain in RIG-I and LGP2, Proceedings of the National Academy of Sciences, vol.104, issue.2, 2007.
DOI : 10.1073/pnas.0606699104

T. Saito, D. Owen, F. Jiang, J. Marcotrigiano, M. Gale et al., Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA, Nature, vol.448, issue.7203, 2008.
DOI : 10.1038/nature07106

T. Satoh, H. Kato, Y. Kumagai, M. Yoneyama, S. Sato et al., LGP2 is a positive regulator of RIG-I- and MDA5-mediated antiviral responses, Proceedings of the National Academy of Sciences, vol.107, issue.4, 2010.
DOI : 10.1073/pnas.0912986107

M. Schlee and G. Hartmann, The Chase for the RIG-I Ligand???Recent Advances, Molecular Therapy, vol.18, issue.7, 2010.
DOI : 10.1038/mt.2010.90

M. Schlee, A. Roth, V. Hornung, C. Hagmann, V. Wimmenauer et al., Recognition of 5??? Triphosphate by RIG-I Helicase Requires Short Blunt Double-Stranded RNA as Contained in Panhandle of Negative-Strand Virus, Immunity, vol.31, issue.1, 2009.
DOI : 10.1016/j.immuni.2009.05.008

A. Schmidt, T. Schwerd, W. Hamm, J. Hellmuth, S. Cui et al., 5'-triphosphate RNA requires basepaired structures to activate antiviral signaling via RIG-I, Proc Natl Acad Sci, 2009.
DOI : 10.1073/pnas.0900971106
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705279

K. Schroder and J. Tschopp, The inflammasomes. Cell, 2010.

F. Scott, B. Stec, C. Pop, M. Dobaczewska, J. Lee et al., The Fas???FADD death domain complex structure unravels signalling by receptor clustering, Nature, vol.11, issue.7232, 2009.
DOI : 10.1038/nature07606

S. Sebastian, C. Grütter, C. Strambio-de-castillia, T. Pertel, S. Olivari et al., An invariant surface patch on the TRIM5alpha PRYSPRY domain is required for retroviral restriction but dispensable for capsid binding, J Virol, 2009.

R. Seth, L. Sun, C. Ea, and Z. Chen, Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3, Cell, 2005.

B. Song, B. Gold, O. Huigin, C. Javanbakht, H. Li et al., The B30.2(SPRY) domain of the retroviral restriction factor TRIM5alpha exhibits lineage-specific length and sequence variation in primates, J Virol, 2005.

L. Storoni, A. Mccoy, and R. Read, Likelihood-enhanced fast rotation functions Activation of the beta interferon promoter by unnatural Sendai virus infection requires RIG-I and is inhibited by viral C proteins, Acta Crystallogr D Biol Crystallogr, 2004.

L. Strähle, J. Marq, A. Brini, S. Hausmann, D. Kolakofsky et al., Activation of the Beta Interferon Promoter by Unnatural Sendai Virus Infection Requires RIG-I and Is Inhibited by Viral C Proteins, Journal of Virology, vol.81, issue.22, 2007.
DOI : 10.1128/JVI.01300-07

F. Studier, Protein production by auto-induction in high-density shaking cultures, Protein Expression and Purification, vol.41, issue.1, 2005.
DOI : 10.1016/j.pep.2005.01.016

R. Sumpter, . Jr, Y. Loo, E. Foy, K. Li et al., Regulating Intracellular Antiviral Defense and Permissiveness to Hepatitis C Virus RNA Replication through a Cellular RNA Helicase, RIG-I, Journal of Virology, vol.79, issue.5, 2005.
DOI : 10.1128/JVI.79.5.2689-2699.2005

A. Takaoka, Z. Wang, M. Choi, H. Yanai, H. Negishi et al., DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator of innate immune response, Nature, vol.84, issue.7152, 2007.
DOI : 10.1038/nature06013

K. Takahasi, H. Kumeta, N. Tsuduki, R. Narita, T. Shigemoto et al., Solution Structures of Cytosolic RNA Sensor MDA5 and LGP2 C-terminal Domains: IDENTIFICATION OF THE RNA RECOGNITION LOOP IN RIG-I-LIKE RECEPTORS, Journal of Biological Chemistry, vol.284, issue.26, 2009.
DOI : 10.1074/jbc.M109.007179

K. Takahasi, M. Yoneyama, T. Nishihori, R. Hirai, H. Kumeta et al., Nonself RNA-Sensing Mechanism of RIG-I Helicase and Activation of Antiviral Immune Responses, Molecular Cell, vol.29, issue.4, 2008.
DOI : 10.1016/j.molcel.2007.11.028

O. Takeuchi and S. Akira, Pattern recognition receptors and inflammation. Cell, 2010.
DOI : 10.1016/j.cell.2010.01.022
URL : http://doi.org/10.1016/j.cell.2010.01.022

O. Takeuchi and S. Akira, Innate immunity to virus infection, Immunological Reviews, vol.451, issue.1, 2009.
DOI : 10.1111/j.1600-065X.2008.00737.x

F. Triana-alonso, M. Dabrowski, J. Wadzack, and K. Nierhaus, Self-coded 3'-extension of run-off transcripts produces aberrant products during in vitro transcription with T7 RNA polymerase, J Biol Chem, 1995.

D. Vitour and E. Meurs, Regulation of interferon production by RIG-I and LGP2 a lesson in self-control. Sci STKE, 2007.

M. Wilkins, E. Gasteiger, A. Bairoch, J. Sanchez, K. Williams et al., Protein Identification and Analysis Tools in the ExPASy Server, Methods Mol Biol, 1999.
DOI : 10.1385/1-59259-584-7:531

T. Venkataraman, M. Valdes, R. Elsby, S. Kakuta, G. Caceres et al., Loss of DExD/H Box RNA Helicase LGP2 Manifests Disparate Antiviral Responses, The Journal of Immunology, vol.178, issue.10, 2007.
DOI : 10.4049/jimmunol.178.10.6444

Y. Wang, J. Ludwig, C. Schuberth, M. Goldeck, M. Schlee et al., Structural and functional insights into 5???-ppp RNA pattern recognition by the innate immune receptor RIG-I, Nature Structural & Molecular Biology, vol.26, issue.7, 2010.
DOI : 10.1038/nsmb.1863

O. Weichenrieder, K. Wild, K. Strub, and S. Cusack, Structure and assembly of the Alu domain of the mammalian signal recognition particle, Nature, 2000.

C. Weinert, C. Grütter, H. Roschitzki-voser, P. Mittl, and M. Gr´-'gr´gr´-'utter, The Crystal Structure of Human Pyrin B30.2 Domain: Implications for Mutations Associated with Familial Mediterranean Fever, Journal of Molecular Biology, vol.394, issue.2, 2009.
DOI : 10.1016/j.jmb.2009.08.059

M. Wilkins, E. Gasteiger, A. Bairoch, J. Sanchez, K. Williams et al., Protein Identification and Analysis Tools in the ExPASy Server, Methods Mol Biol, 1999.
DOI : 10.1385/1-59259-584-7:531

J. Woo, J. Imm, C. Min, K. Kim, S. Cha et al., Structural and functional insights into the B30.2/SPRY domain, The EMBO Journal, vol.37, issue.6, 2006.
DOI : 10.1016/j.abb.2003.11.017

J. Woo, H. Suh, S. Park, and B. Oh, Structural Basis for Protein Recognition by B30.2/SPRY Domains, Molecular Cell, vol.24, issue.6, 2006.
DOI : 10.1016/j.molcel.2006.11.009

L. Xu, Y. Wang, K. Han, L. Li, Z. Zhai et al., VISA is an adapter protein required for virus-triggered IFN-beta signaling, Mol Cell, 2005.

N. Yan, J. Chai, E. Lee, L. Gu, Q. Liu et al., Structure of the CED-4???CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans, Nature, vol.11, issue.7060
DOI : 10.1107/S0021889891004399

M. Yoneyama, M. Kikuchi, T. Natsukawa, N. Shinobu, T. Imaizumi et al., The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses, Nature Immunology, vol.120, issue.7, 2004.
DOI : 10.1038/ni910

M. Yoneyama and T. Fujita, RNA recognition and signal transduction by RIG-I-like receptors, Immunological Reviews, vol.282, issue.1, 2009.
DOI : 10.1111/j.1600-065X.2008.00727.x

S. Yuan, X. Yu, M. Topf, S. Ludtke, X. Wang et al., Structure of an Apoptosome-Procaspase-9 CARD Complex, Structure, vol.18, issue.5, 2010.
DOI : 10.1016/j.str.2010.04.001

W. Zeng, L. Sun, X. Jiang, X. Chen, F. Hou et al., Reconstitution of the RIG-I Pathway Reveals a Signaling Role of Unanchored Polyubiquitin Chains in Innate Immunity, Cell, vol.141, issue.2, 2010.
DOI : 10.1016/j.cell.2010.03.029

C. Zhao, C. Denison, J. Huibregtse, S. Gygi, and R. Krug, Human ISG15 conjugation targets both IFN-induced and constitutively expressed proteins functioning in diverse cellular pathways, Proceedings of the National Academy of Sciences, vol.102, issue.29, 2005.
DOI : 10.1073/pnas.0504754102

B. Zimm, The Scattering of Light and the Radial Distribution Function of High Polymer Solutions, The Journal of Chemical Physics, vol.16, issue.12, 1948.
DOI : 10.1063/1.1746738

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, 2003.
DOI : 10.1093/nar/gkg595