A. B. Abecasis, A. Vandamme, and P. Lemey, Quantifying Differences in the Tempo of Human Immunodeficiency Virus Type 1 Subtype Evolution, Journal of Virology, vol.83, issue.24, pp.12917-12924, 2009.
DOI : 10.1128/JVI.01022-09

A. F. Aghokeng, E. Mpoudi-ngole, H. Dimodi, A. Atem-tambe, and M. ,

M. Delaporte and . Peeters, Inaccurate Diagnosis of HIV-1 Group M and O Is a Key Challenge for Ongoing Universal Access to Antiretroviral Treatment and HIV Prevention in Cameroon, PLOS ONE, vol.4, issue.11, p.7702, 2009.

, Stages of HIV Infection, AIDS.gov, 2015.

. Aidsinfo, The Stages of HIV Infection, 2016.

J. Archer, J. W. Pinney, J. Fan, E. Simon-loriere, E. J. Arts et al., Identifying the Important HIV-1 Recombination Breakpoints, PLoS Computational Biology, vol.4, issue.9, p.1000178, 2008.
DOI : 10.1371/journal.pcbi.1000178.g004
URL : https://hal.archives-ouvertes.fr/hal-00356326

K. K. Ariën, A. Abraha, M. E. Quiñones-mateu, L. Kestens, G. Vanham et al., The Replicative Fitness of Primary Human Immunodeficiency Virus Type, 2005.

M. Group and . Hiv-, 1 Group O, and HIV-2 Isolates, Journal of Virology, vol.79, issue.14, pp.8979-8990

L. O. Arthur, J. W. Bess, R. C. Sowder, R. E. Benveniste, D. L. Mann et al., Cellular proteins bound to immunodeficiency viruses: implications for pathogenesis and vaccines, Science, vol.258, issue.5090, p.1935, 1992.
DOI : 10.1126/science.1470916

N. Asherie, Protein crystallization and phase diagrams, Methods, vol.34, issue.3, pp.266-272, 2004.
DOI : 10.1016/j.ymeth.2004.03.028

J. M. Baeten, B. Chohan, L. Lavreys, V. Chohan, R. S. Mcclelland et al.,

W. Mandaliya, O. Jaoko, and . Julie, HIV-1 Subtype D Infection Is Associated with Faster Disease Progression than Subtype A in Spite of Similar Plasma HIV-1 Loads, The Journal of Infectious Diseases, vol.195, issue.8, pp.1177-1180, 2007.

R. Baid, A. K. Upadhyay, T. Shinohara, and U. B. Kompella, ), a Novel Therapeutic Protein, Journal of Biological Chemistry, vol.66, issue.24, pp.17372-17383, 2013.
DOI : 10.1007/s00894-009-0555-5

C. Barat, V. Lullien, O. Schatz, G. Keith, M. T. Nugeyre et al.,

S. F. Sinoussi, J. L. Legrice, and . Darlix, HIV-1 reverse transcriptase specifically interacts with the anticodon domain of its cognate primer tRNA, The EMBO Journal, vol.8, issue.11, pp.3279-3285, 1989.

F. Barre-sinoussi, J. C. Chermann, F. Rey, and M. T. ,

C. Dauguet, F. Axler-blin, C. Vezinet-brun, W. Rouzioux, L. Rozenbaum et al., Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS), Science, vol.220, issue.4599, p.868, 1983.

M. S. Benleulmi, J. Matysiak, D. R. Henriquez, C. Vaillant, and P. ,

O. Naughtin, A. M. Leon, M. Skalka, M. Ruff, M. L. Lavigne et al., Intasome architecture and chromatin density modulate retroviral integration into nucleosome, Retrovirology, vol.12, p.13, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01416843

P. D. Bieniasz, T. A. Grdina, H. P. Bogerd, and B. R. Cullen, Recruitment of a protein complex containing Tat and cyclin T1 to TAR governs the species specificity of HIV-1 Tat, The EMBO Journal, vol.11, issue.23, 1998.
DOI : 10.1101/gad.11.20.2622

. Tat, The EMBO Journal, vol.17, issue.23, pp.7056-7065

A. A. Bothner and R. Gassend, BINDING OF SMALL MOLECULES TO PROTEINS, Annals of the New York Academy of Sciences, vol.513, issue.1 Electron Spin, pp.668-676, 1973.
DOI : 10.1016/0022-2836(69)90426-4

C. L. Boutwell, J. M. Carlson, T. Lin, A. Seese, K. A. Power et al.,

D. Brumme, A. Heckerman, T. M. Schneidewind, and . Allen, Frequent and Variable Cytotoxic-T-Lymphocyte Escape-Associated Fitness Costs in the Human Immunodeficiency Virus Type 1 Subtype B Gag Proteins, Journal of Virology, vol.87, issue.7, pp.3952-3965, 2013.

C. L. Boutwell, C. F. Rowley, and M. Essex, Reduced Viral Replication Capacity of Human Immunodeficiency Virus Type 1 Subtype C Caused by Cytotoxic-T-Lymphocyte Escape Mutations in HLA-B57 Epitopes of Capsid Protein, Journal of Virology, vol.83, issue.6, pp.2460-2468, 2009.
DOI : 10.1128/JVI.01970-08

J. A. Briggs, J. D. Riches, B. Glass, V. Bartonova, G. Zanetti et al., Structure and assembly of immature HIV, Proceedings of the National Academy of Sciences, vol.164, issue.1, pp.11090-11095, 2009.
DOI : 10.1016/j.jsb.2008.05.003

M. I. Bukrinsky, N. Sharova, M. P. Dempsey, T. L. Stanwick, and A. G. ,

M. Haggerty and . Stevenson, Active nuclear import of human immunodeficiency virus type 1 preintegration complexes, Proceedings of the National Academy of Sciences of the United States of America, vol.89, issue.14, pp.6580-6584, 1992.

F. D. Bushman, A. Engelman, I. Palmer, P. Wingfield, and R. Craigie, Domains of the integrase protein of human immunodeficiency virus type 1 responsible for polynucleotidyl transfer and zinc binding., Proceedings of the National Academy of Sciences, vol.90, issue.8, pp.3428-3432, 1993.
DOI : 10.1073/pnas.90.8.3428

F. D. Bushman, T. Fujiwara, and R. Craigie, Retroviral DNA integration directed by HIV integration protein in vitro, Science, vol.249, issue.4976, p.1555, 1990.
DOI : 10.1126/science.2171144

K. Busschots, J. Vercammen, S. Emiliani, R. Benarous, Y. Engelborghs et al.,

. Debyser, The interaction of LEDGF/p75 with integrase is lentivirus-specific and promotes DNA binding, J Biol Chem, vol.280, 2005.

M. Cai, R. Zheng, M. Caffrey, R. Craigie, G. M. Clore et al., , 1997.

, Solution structure of the N-terminal zinc binding domain of HIV-1 integrase, Nat Struct Mol Biol, vol.4, issue.7, pp.567-577

R. Cancio, S. Spadari, and G. Maga, Vif is an auxiliary factor of the HIV-1 reverse transcriptase and facilitates abasic site bypass, Biochemical Journal, vol.383, issue.3, p.475, 2004.
DOI : 10.1042/BJ20040914

J. M. Carlson, A. Q. Le, A. Shahid, and Z. L. Brumme, HIV-1 adaptation to HLA: a window into virus???host immune interactions, Trends in Microbiology, vol.23, issue.4, pp.212-224, 2015.
DOI : 10.1016/j.tim.2014.12.008

L. Carlson, J. A. Briggs, B. Glass, J. D. Riches, M. N. Simon et al.,

K. Müller, H. Grünewald, and . Kräusslich, Three-Dimensional Analysis of Budding Sites and Released Virus Suggests a Revised Model for HIV-1 Morphogenesis, Cell Host & Microbe, vol.4, issue.6, pp.592-599, 2008.

J. Cavanagh, W. J. Fairbrother, A. G. Palmer-iii, M. Rance, and N. J. Skelton, , 2007.

-. Experiments, CHAPTER Protein NMR Spectroscopy, pp.533-678

, CDC, 2016.

N. E. Chayen and E. Saridakis, Protein crystallization: from purified protein to diffraction-quality crystal, Nature Methods, vol.286, issue.2, pp.147-153, 2008.
DOI : 10.1038/nmeth.f.203

M. A. Checkley, B. G. Luttge, and E. O. Freed, HIV-1 Envelope Glycoprotein Biosynthesis, Trafficking, and Incorporation, Journal of Molecular Biology, vol.410, issue.4, pp.582-608, 2011.
DOI : 10.1016/j.jmb.2011.04.042
URL : http://europepmc.org/articles/pmc3139147?pdf=render

A. Chen, I. T. Weber, R. W. Harrison, and J. Leis, Identification of Amino Acids in HIV-1 and Avian Sarcoma Virus Integrase Subsites Required for Specific Recognition of the Long Terminal Repeat Ends, Journal of Biological Chemistry, vol.281, issue.7, pp.4173-4182, 2006.
DOI : 10.1074/jbc.M510628200

C. Chen, T. J. Nott, J. Jin, and T. Pawson, Deciphering arginine methylation: Tudor tells the tale, Nature Reviews Molecular Cell Biology, vol.14, issue.10, pp.629-642, 2011.
DOI : 10.1016/j.str.2005.09.018

J. C. Chen, J. Krucinski, L. J. Miercke, J. S. Finer-moore, A. H. Tang et al., Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: A model for viral DNA binding, Proceedings of the National Academy of Sciences, vol.50, issue.Pt 5, pp.8233-8238, 2000.
DOI : 10.1107/S0907444994003112

P. Cherepanov, LEDGF/p75 interacts with divergent lentiviral integrases and modulates their enzymatic activity in vitro, Nucleic Acids Research, vol.31, issue.1, pp.113-124, 2007.
DOI : 10.1093/nar/gkg556

P. Cherepanov, A. L. Ambrosio, S. Rahman, T. Ellenberger, and A. Engelman, , 2005.

, Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75, Proceedings of the National Academy of Sciences of the United States of America, vol.102, issue.48, pp.17308-17313

P. Cherepanov, E. Devroe, P. A. Silver, and A. Engelman, Identification of an Evolutionarily Conserved Domain in Human Lens Epithelium-derived Growth Factor/Transcriptional Co-activator p75 (LEDGF/p75) That Binds HIV-1 Integrase, Journal of Biological Chemistry, vol.73, issue.47, pp.48883-48892, 2004.
DOI : 10.1093/bioinformatics/15.4.305

P. Cherepanov, G. Maertens, P. Proost, B. Devreese, J. Van-beeumen et al., HIV-1 Integrase Forms Stable Tetramers and Associates with LEDGF/p75 Protein in Human Cells, Journal of Biological Chemistry, vol.40, issue.1, 2003.
DOI : 10.1002/bms.1200111109

P. Cherepanov, Z. J. Sun, S. Rahman, G. Maertens, G. Wagner et al., , 2005.

, Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75, Nat Struct Mol Biol, vol.12, issue.6, pp.526-532

M. Cheung, M. L. Maguire, T. J. Stevens, and R. W. Broadhurst, DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure, Journal of Magnetic Resonance, vol.202, issue.2, pp.223-233, 2010.
DOI : 10.1016/j.jmr.2009.11.008

S. A. Chow, K. A. Vincent, V. Ellison, and P. O. Brown, Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus, Science, vol.255, issue.5045, 1992.
DOI : 10.1126/science.1738845

T. Cihlar and M. Fordyce, Current status and prospects of HIV treatment, Current Opinion in Virology, vol.18, pp.50-56, 2016.
DOI : 10.1016/j.coviro.2016.03.004

A. Ciuffi, M. Llano, E. Poeschla, C. Hoffmann, J. Leipzig et al., J. R. Ecker and F

, A role for LEDGF/p75 in targeting HIV DNA integration, Bushman Nat Med, vol.11, 2005.

P. R. Clapham and Á. Mcknight, Cell surface receptors, virus entry and tropism of primate lentiviruses, Journal of General Virology, vol.393, issue.8, pp.1809-1829, 2002.
DOI : 10.1038/31269

J. Coffin and R. Swanstrom, HIV Pathogenesis: Dynamics and Genetics of Viral Populations and Infected Cells, Cold Spring Harbor Perspectives in Medicine, vol.3, issue.1, p.12526, 2013.
DOI : 10.1101/cshperspect.a012526

M. S. Cohen, G. M. Shaw, A. J. Mcmichael, and B. F. Haynes, , 2011.

, Infection The New England journal of medicine, vol.364, issue.20, pp.1943-1954

M. Cong, W. Heneine, and J. G. García-lerma, The Fitness Cost of Mutations Associated with Human Immunodeficiency Virus Type 1 Drug Resistance Is Modulated by Mutational Interactions, Journal of Virology, vol.81, issue.6, pp.3037-3041, 2007.
DOI : 10.1128/JVI.02712-06

R. Craigie and F. D. Bushman, HIV DNA Integration, Cold Spring Harbor Perspectives in Medicine, vol.2, issue.7, 2012.
DOI : 10.1101/cshperspect.a006890

J. M. Cuevas, R. Geller, R. Garijo, J. López-aldeguer, and R. Sanjuán, Extremely High Mutation Rate of HIV-1 In Vivo, PLOS Biology, vol.8, issue.9, p.1002251, 2015.
DOI : 10.1371/journal.pbio.1002251.s011

M. Dahabieh, E. Battivelli, and E. Verdin, Understanding HIV Latency: The Road to an HIV Cure, Annual Review of Medicine, vol.66, issue.1, pp.407-421, 2015.
DOI : 10.1146/annurev-med-092112-152941

C. Dalvit, G. Fogliatto, A. Stewart, M. Veronesi, and B. Stockman, WaterLOGSY as a method for primary NMR screening: Practical aspects and range of applicability, Journal of Biomolecular NMR, vol.21, issue.4, pp.349-359, 2001.
DOI : 10.1023/A:1013302231549

J. De-rijck, C. De-kogel, J. Demeulemeester, S. Vets, S. E. Ashkar et al.,

B. Bushman, S. J. Landuyt, K. Husson, R. Busschots, Z. Gijsbers et al., The BET family of proteins targets Moloney Murine Leukemia Virus integration near transcription start sites, Cell reports, vol.5, issue.4, pp.886-894, 2013.

W. L. Delano, The PyMOL Molecular Graphics System, 2002.

D. Primio, C. , V. Quercioli, A. Allouch, R. Gijsbers et al., Z. Debyser, D. Arosio and A

, Single-Cell Imaging of HIV-1 Provirus (SCIP), Cereseto Proceedings of the National Academy of Sciences, vol.110, issue.14, pp.5636-5641, 2013.

C. Dominguez, R. Boelens, and A. M. Bonvin, HADDOCK:?? A Protein???Protein Docking Approach Based on Biochemical or Biophysical Information, Journal of the American Chemical Society, vol.125, issue.7, pp.1731-1737, 2003.
DOI : 10.1021/ja026939x

F. Dyda, A. B. Hickman, T. M. Jenkins, A. Engelman, R. Craigie et al., , 1994.

, Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases, Science, vol.266, issue.5193, p.1981

J. O. Eidahl, B. L. Crowe, J. A. North, C. J. Mckee, N. Shkriabai et al.,

R. J. Graham, S. Gorelick, M. G. Hess, M. P. Poirier, M. Foster et al., , 2013.

, Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes, Nucleic Acids Research, vol.41, issue.6, pp.3924-3936

A. P. Eijkelenboom, R. A. Puras-lutzke, R. Boelens, R. H. Plasterk, R. Kaptein et al., The DNA-binding domain of HIV-1 integrase has an SH3-like fold, Nature Structural & Molecular Biology, vol.22, issue.9, pp.807-810, 1995.
DOI : 10.1107/S0021889891004399

P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan, Features and development of Coot, Acta Crystallogr D Biol Crystallogr, vol.66, 2010.

A. Engelman, G. Englund, J. M. Orenstein, M. A. Martin, and R. Craigie, Multiple effects of mutations in human immunodeficiency virus type 1 integrase on viral replication, Journal of Virology, vol.69, issue.5, pp.2729-2736, 1995.

A. Engelman, J. J. Kessl, and M. Kvaratskhelia, Allosteric inhibition of HIV-1, 2013.
DOI : 10.1016/j.cbpa.2013.04.010
URL : http://europepmc.org/articles/pmc3679204?pdf=render

, Current opinion in chemical biology, vol.17, issue.3, pp.339-345

A. Engelman, K. Mizuuchi, and R. Craigie, HIV-1 DNA integration: Mechanism of viral DNA cleavage and DNA strand transfer, Cell, vol.67, issue.6, pp.1211-1221, 1991.
DOI : 10.1016/0092-8674(91)90297-C

J. J. Eron, HIV-1 Protease Inhibitors, Clinical Infectious Diseases, vol.13, issue.(RR-5), pp.160-170, 2000.
DOI : 10.1097/00002030-199909100-00009

F. D. , Antiretroviral drugs used in the treatment of HIV infection, 2016.

B. T. Farmer, R. A. Venters, L. D. Spicer, M. G. Wittekind, and L. Müller, A refocused and optimized HNCA: Increased sensitivity and resolution in large macromolecules, Journal of Biomolecular NMR, vol.64, issue.2, pp.195-202, 1992.
DOI : 10.1016/0022-2364(85)90122-2

A. Fassati and S. P. Goff, Characterization of Intracellular Reverse Transcription Complexes of Human Immunodeficiency Virus Type 1, Journal of Virology, vol.75, issue.8, pp.3626-3635, 2001.
DOI : 10.1128/JVI.75.8.3626-3635.2001

M. A. Fischl, D. D. Richman, M. H. Grieco, M. S. Gottlieb, P. A. Volberding et al., The Efficacy of Azidothymidine (AZT) in the Treatment of Patients with AIDS and AIDS-Related Complex, New England Journal of Medicine, vol.317, issue.4, pp.185-191, 1987.
DOI : 10.1056/NEJM198707233170401

B. M. Forshey, U. Von-schwedler, W. I. Sundquist, and C. Aiken, Formation of a Human Immunodeficiency Virus Type 1 Core of Optimal Stability Is Crucial for Viral Replication, Journal of Virology, vol.76, issue.11, pp.5667-5677, 2002.
DOI : 10.1128/JVI.76.11.5667-5677.2002

A. D. Frankel and J. A. Young, HIV-1: Fifteen Proteins and an RNA, Annual Review of Biochemistry, vol.67, issue.1, pp.1-25, 1998.
DOI : 10.1146/annurev.biochem.67.1.1

E. O. Freed, HIV-1 assembly, release and maturation, Nature Reviews Microbiology, vol.343, issue.8, pp.484-496, 2015.
DOI : 10.1126/science.1247786

K. Fujinaga, T. P. Cujec, and J. Peng, , 1998.

, The Ability of Positive Transcription Elongation Factor b To Transactivate Human Immunodeficiency Virus Transcription Depends on a Functional Kinase Domain, Cyclin T1, and Tat, Journal of Virology, vol.72, issue.9, pp.7154-7159

B. Ganser-pornillos, M. Yeager, and W. I. Sundquist, The structural biology of HIV assembly, Current Opinion in Structural Biology, vol.18, issue.2, p.203, 2008.
DOI : 10.1016/j.sbi.2008.02.001

F. Gao, E. Bailes, D. L. Robertson, Y. Chen, C. M. Rodenburg et al.,

L. O. Cummins, M. Arthur, G. M. Peeters, P. M. Shaw, B. H. Sharp et al., Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes, Nature, vol.397, issue.6718, pp.436-441, 1999.

M. L. Greenberg and N. Cammack, Resistance to enfuvirtide, the first HIV fusion inhibitor, Journal of Antimicrobial Chemotherapy, vol.54, issue.2, pp.333-340, 2004.
DOI : 10.1093/jac/dkh330

N. J. Greenfield, Using circular dichroism spectra to estimate protein secondary structure, Nature Protocols, vol.79, issue.6, pp.2876-2890, 2006.
DOI : 10.1016/j.bbapap.2005.06.005

J. Greenwald, V. Le, S. L. Butler, F. D. Bushman, and S. Choe, Biochemistry, vol.38, issue.28, pp.8892-8898, 1999.
DOI : 10.1021/bi9907173

S. Grzesiek and A. Bax, Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR, Journal of the American Chemical Society, vol.114, issue.16, pp.6291-6293, 1992.
DOI : 10.1021/ja00042a003

S. Grzesiek and A. Bax, An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins, Journal of Magnetic Resonance (1969), vol.99, issue.1, pp.201-207, 1969.
DOI : 10.1016/0022-2364(92)90169-8
URL : https://zenodo.org/record/1253928/files/article.pdf

S. S. Gupta, T. Maetzig, G. N. Maertens, A. Sharif, M. Rothe et al., Bromo- and Extraterminal Domain Chromatin Regulators Serve as Cofactors for Murine Leukemia Virus Integration, Journal of Virology, vol.87, issue.23, pp.12721-12736, 2013.
DOI : 10.1128/JVI.01942-13
URL : http://jvi.asm.org/content/87/23/12721.full.pdf

B. H. Hahn, G. M. Shaw, K. M. De, C. , and P. M. Sharp, AIDS as a Zoonosis: Scientific and Public Health Implications, Science, vol.287, issue.5453, p.607, 2000.
DOI : 10.1126/science.287.5453.607

N. K. Heinzinger, M. I. Bukinsky, S. A. Haggerty, A. M. Ragland, V. Kewalramani et al.,

H. E. Lee, L. Gendelman, M. Ratner, M. Stevenson, and . Emerman, The Vpr protein of human immunodeficiency virus type 1 influences nuclear localization of viral nucleic acids in nondividing host cells, Proceedings of the National Academy of Sciences, vol.91, issue.15, pp.7311-7315, 1994.

J. Hemelaar, The origin and diversity of the HIV-1 pandemic, Trends in Molecular Medicine, vol.18, issue.3, pp.182-192, 2012.
DOI : 10.1016/j.molmed.2011.12.001

T. J. Henrich and D. R. Kuritzkes, HIV-1 entry inhibitors: recent development and clinical use, Current Opinion in Virology, vol.3, issue.1, pp.51-57, 2013.
DOI : 10.1016/j.coviro.2012.12.002

C. Hicks and R. M. Gulick, Raltegravir: The First HIV Type 1, 2009.

I. Inhibitor, Clinical Infectious Diseases, vol.48, issue.7, pp.931-939

V. Higman, Spectrum Descriptions, 2012.

Z. Hu and D. R. Kuritzkes, Altered Viral Fitness and Drug Susceptibility in HIV-1, 2014.

, Carrying Mutations That Confer Resistance to Nonnucleoside Reverse Transcriptase and Integrase Strand Transfer Inhibitors, Journal of Virology, vol.88, issue.16, pp.9268-9276

A. E. Hulme, Z. Kelley, D. Foley, and T. J. Hope, ABSTRACT, Journal of Virology, vol.89, issue.10, pp.5350-5361, 2015.
DOI : 10.1128/JVI.00476-15

, Gateway Technology, Invitrogen, 2003.

C. Isel and J. Karn, Direct evidence that HIV-1 tat stimulates RNA polymerase II carboxyl-terminal domain hyperphosphorylation during transcriptional elongation, Journal of Molecular Biology, vol.290, issue.5, pp.929-941, 1999.
DOI : 10.1006/jmbi.1999.2933

C. Jain and J. G. Belasco, Structural Model for the Cooperative Assembly of HIV-1, 2001.

, Rev Multimers on the RRE as Deduced from Analysis of Assembly-Defective Mutants, Molecular Cell, vol.7, issue.3, pp.603-614

T. M. Jenkins, D. Esposito, A. Engelman, and R. Craigie, Critical contacts between HIV-1 integrase and viral DNA identified by structure-based analysis and photo-crosslinking, The EMBO Journal, vol.16, issue.22, pp.6849-6859, 1997.
DOI : 10.1093/emboj/16.22.6849

T. M. Jenkins, A. B. Hickman, F. Dyda, R. Ghirlando, D. R. Davies et al., , 1995.

, Catalytic domain of human immunodeficiency virus type 1 integrase: identification of a soluble mutant by systematic replacement of hydrophobic residues, Proc Natl Acad Sci

M. Jerabek-willemsen, T. André, R. Wanner, H. M. Roth, and S. Duhr,

, MicroScale Thermophoresis: Interaction analysis and beyond, Breitsprecher Journal of Molecular Structure, vol.1077, pp.101-113, 2014.

M. Jerabek-willemsen, C. J. Wienken, D. Braun, P. Baaske, and S. Duhr, Molecular Interaction Studies Using Microscale Thermophoresis, ASSAY and Drug Development Technologies, vol.9, issue.4, pp.342-353, 2011.
DOI : 10.1089/adt.2011.0380

L. E. Kay, M. Ikura, R. Tschudin, and A. Bax, Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins, Journal of Magnetic Resonance, vol.89, issue.3, pp.496-514, 1969.

S. M. Kelly, T. J. Jess, and N. C. Price, How to study proteins by circular dichroism, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1751, issue.2, pp.119-139, 2005.
DOI : 10.1016/j.bbapap.2005.06.005

S. Khurshid, E. Saridakis, L. Govada, and N. E. Chayen, Porous nucleating agents for protein crystallization, Nature Protocols, vol.9, issue.7, pp.1621-1633, 2014.
DOI : 10.1038/nmeth742

D. Kim, B. J. Blus, V. Chandra, P. Huang, F. Rastinejad et al., , 2010.

, Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain, Nat Struct Mol Biol, vol.17, issue.8, pp.1027-1029

J. Kim, J. Daniel, A. Espejo, A. Lake, M. Krishna et al., Tudor, MBT and chromo domains gauge the degree of lysine methylation, EMBO reports, vol.62, issue.4, pp.397-403, 2006.
DOI : 10.1128/MCB.25.15.6404-6414.2005

C. Köhler, R. Recht, M. Quinternet, and F. , , 2015.

, Accurate Protein?Peptide Titration Experiments by Nuclear Magnetic Resonance Using

, Affinity Chromatography: Methods and Protocols. S. Reichelt, pp.279-296

L. Krishnan, X. Li, H. L. Naraharisetty, S. Hare, P. Cherepanov et al., , 2010.

, Structure-based modeling of the functional HIV-1 intasome and its inhibition, Proceedings of the National Academy of Sciences, vol.107, issue.36, pp.15910-15915

E. Krissinel and K. Henrick, Inference of Macromolecular Assemblies from Crystalline State, Journal of Molecular Biology, vol.372, issue.3, pp.774-797, 2007.
DOI : 10.1016/j.jmb.2007.05.022

P. D. Kwong, R. Wyatt, J. Robinson, R. W. Sweet, J. Sodroski et al., Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody, Nature, vol.11, issue.6686, pp.648-659, 1998.
DOI : 10.1002/prot.340110407

L. Noury, D. A. , S. Mosebi, M. A. Papathanasopoulos, and R. Hewer, Functional roles of HIV-1 Vpu and CD74: Details and implications of the Vpu???CD74 interaction, Cellular Immunology, vol.298, issue.1-2, pp.25-32, 2015.
DOI : 10.1016/j.cellimm.2015.08.005

L. Rouzic, E. , D. Bonnard, S. Chasset, J. Bruneau et al.,

A. Saïb, S. Zamborlini, M. Emiliani, B. Ruff, F. Ledoussal et al., , 2013.

, Dual inhibition of HIV-1 replication by integrase-LEDGF allosteric inhibitors is predominant at the post-integration stage, Retrovirology, vol.10, issue.1, p.144

D. J. Leibly, T. N. Nguyen, L. T. Kao, S. N. Hewitt, L. K. Barrett et al., Stabilizing Additives Added during Cell Lysis Aid in the Solubilization of Recombinant Proteins, PLoS ONE, vol.8, issue.3, p.52482, 2012.
DOI : 10.1371/journal.pone.0052482.t004

P. Lesbats, A. N. Engelman, and P. Cherepanov, Retroviral DNA Integration, Chemical Reviews, vol.116, issue.20, pp.12730-12757, 2016.
DOI : 10.1021/acs.chemrev.6b00125

R. J. Lessells, D. K. Katzenstein, and T. De-oliveira, Are subtype differences important in HIV drug resistance?, Current Opinion in Virology, vol.2, issue.5, pp.636-643, 2012.
DOI : 10.1016/j.coviro.2012.08.006

P. Lewis, M. Hensel, and M. Emerman, Human immunodeficiency virus infection of cells arrested in the cell cycle, The EMBO Journal, vol.11, issue.8, pp.3053-3058, 1992.

J. Liu, A. Bartesaghi, M. J. Borgnia, G. Sapiro, and S. Subramaniam, Molecular architecture of native HIV-1 gp120 trimers, Nature, vol.157, issue.7209, pp.109-113, 2008.
DOI : 10.1038/nature07159

M. Llano, S. Delgado, M. Vanegas, and E. M. Poeschla, Lens Epithelium-derived Growth Factor/p75 Prevents Proteasomal Degradation of HIV-1 Integrase, Journal of Biological Chemistry, vol.72, issue.53, pp.55570-55577, 2004.
DOI : 10.1126/science.1083413

M. Llano, D. T. Saenz, A. Meehan, P. Wongthida, M. Peretz et al.,

M. Poeschla, An Essential Role for LEDGF/p75 in HIV Integration, Science, vol.314, issue.5798, p.461, 2006.

M. Llano, M. Vanegas, O. Fregoso, D. Saenz, S. Chung et al., LEDGF/p75 Determines Cellular Trafficking of Diverse Lentiviral but Not Murine Oncoretroviral Integrase Proteins and Is a Component of Functional Lentiviral Preintegration Complexes, Journal of Virology, vol.78, issue.17, pp.9524-9537, 2004.
DOI : 10.1128/JVI.78.17.9524-9537.2004

M. Llano, M. Vanegas, N. Hutchins, D. Thompson, S. Delgado et al., , 2006.

, Identification and Characterization of the Chromatin-binding Domains of the HIV-1

I. Interactor and L. /. , Journal of Molecular Biology, vol.360, issue.4, pp.760-773

P. J. Lodi, J. A. Ernst, J. Kuszewski, A. B. Hickman, A. Engelman et al., , 1995.

. Integrase, Biochemistry, vol.34, issue.31, pp.9826-9833

R. A. Lutzke, C. Vink, and R. H. Plasterk, Characterization of the minimal DNA-binding domain of the HIV integrase protein, Nucleic Acids Research, vol.22, issue.20, pp.4125-4131, 1994.
DOI : 10.1093/nar/22.20.4125

G. Maertens and P. Cherepanov, Z. Debyser, Y. Engelborghs and A. Engelman, 2004.

, Identification and Characterization of a Functional Nuclear Localization Signal in the HIV-1

I. Interactor and L. /. , Journal of Biological Chemistry, vol.279, issue.32, pp.33421-33429

G. Maertens, P. Cherepanov, W. Pluymers, K. Busschots, and E. De-clercq, Z. Debyser and Y

, LEDGF/p75 Is Essential for Nuclear and Chromosomal Targeting of HIV-1 Integrase in Human Cells, Engelborghs Journal of Biological Chemistry, vol.278, issue.35, pp.33528-33539, 2003.

B. Maillot, N. Lévy, S. Eiler, C. Crucifix, F. Granger et al.,

S. Pradeau-aubreton, A. Emiliani, P. Nazabal, V. Lesbats, Y. Parissi et al., Structural and Functional Role of INI1 and LEDGF in the HIV- 1 Preintegration Complex, PLOS ONE, vol.8, issue.4, p.60734, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01101113

S. Malhotra, O. K. Mathew, and R. Sowdhamini, DOCKSCORE: a webserver for ranking protein-protein docked poses, BMC Bioinformatics, vol.369, issue.Web Server issu, p.127, 2015.
DOI : 10.1016/j.jmb.2007.03.077

B. Marini, A. Kertesz-farkas, H. Ali, B. Lucic, K. Lisek et al.,

A. Luzzati, F. Recchia, M. Mavilio, M. Giacca, and . Lusic, Nuclear architecture dictates HIV-1 integration site selection, Nature, vol.521, issue.7551, pp.227-231, 2015.

D. Marion, P. C. Driscoll, L. E. Kay, P. T. Wingfield, A. Bax et al.,

, Overcoming the overlap problem in the assignment of proton NMR spectra of larger proteins by use of three-dimensional heteronuclear proton-nitrogen-15 Hartmann- Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: application to interleukin 1.beta, Clore Biochemistry, vol.28, issue.15, pp.6150-6156, 1989.

D. Marion, L. E. Kay, S. W. Sparks, D. A. Torchia, and A. Bax, Three-dimensional heteronuclear NMR of nitrogen-15 labeled proteins, Journal of the American Chemical Society, vol.111, issue.4, pp.1515-1517, 1989.
DOI : 10.1021/ja00186a066

S. R. Martin and P. M. Bayley, Absorption and Circular Dichroism Spectroscopy, 2002.
DOI : 10.1385/1-59259-184-1:043

, Calcium-Binding Protein Protocols

N. Totowa, , pp.43-55

D. P. Maskell, L. Renault, E. Serrao, P. Lesbats, R. Matadeen et al.,

A. Engelman, P. Costa, and . Cherepanov, Structural basis for retroviral integration into nucleosomes, Nature, vol.523, issue.7560, pp.366-369, 2015.

K. A. Matreyek and A. Engelman, Viral and Cellular Requirements for the Nuclear Entry of Retroviral Preintegration Nucleoprotein Complexes, Viruses, vol.177, issue.10, pp.2483-2511, 2013.
DOI : 10.1016/j.chom.2010.08.006

K. A. Matreyek, S. S. Yücel, X. Li, and A. Engelman, Nucleoporin NUP153 Phenylalanine-Glycine Motifs Engage a Common Binding Pocket within the HIV-1 Capsid Protein to Mediate Lentiviral Infectivity, PLoS Pathogens, vol.279, issue.10, p.1003693, 2013.
DOI : 10.1371/journal.ppat.1003693.s005

L. P. Mcintosh and F. W. Dahlquist, Biosynthetic Incorporation of 15N and 13C for Assignment and Interpretation of Nuclear Magnetic Resonance Spectra of Proteins, Quarterly Reviews of Biophysics, vol.69, issue.01, pp.1-38, 2009.
DOI : 10.1021/bi00401a022

M. W. Mcnatt, T. Zang, and P. D. Bieniasz, Vpu Binds Directly to Tetherin and Displaces It from Nascent Virions, PLoS Pathogens, vol.7, issue.4, p.1003299, 2013.
DOI : 10.1371/journal.ppat.1003299.s003

T. Mesplede, P. K. Quashie, N. Osman, Y. Han, D. N. Singhroy et al., Viral fitness cost prevents HIV-1 from evading dolutegravir drug pressure, Retrovirology, vol.10, issue.1, 2013.
DOI : 10.1038/nature08784

F. Michel, C. Crucifix, F. Granger, S. Eiler, J. F. Mouscadet et al.,

M. Ziganshin, A. Gottikh, and . Nazabal, Structural basis for HIV-1 DNA integration in the human genome, role of the LEDGF/P75 cofactor, EMBO J, vol.28, 2009.
URL : https://hal.archives-ouvertes.fr/inserm-00384501

M. D. Miller, C. M. Farnet, and F. D. Bushman, Human immunodeficiency virus type 1 preintegration complexes: studies of organization and composition, Journal of Virology, vol.71, issue.7, pp.5382-5390, 1997.

R. S. Mitchell, B. F. Beitzel, A. R. Schroder, P. Shinn, H. Chen et al., Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences, Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences, p.234, 2004.
DOI : 10.1371/journal.pbio.0020234.sd002
URL : http://doi.org/10.1371/journal.pbio.0020234

Y. Morikawa, D. J. Hockley, M. V. Nermut, and I. M. Jones, Roles of Matrix, p2, and N-Terminal Myristoylation in Human Immunodeficiency Virus Type 1 Gag Assembly, Journal of Virology, vol.74, issue.1, pp.16-23, 2000.
DOI : 10.1128/JVI.74.1.16-23.2000
URL : http://jvi.asm.org/content/74/1/16.full.pdf

C. G. Moscoso, Y. Sun, S. Poon, L. Xing, E. Kan et al., Quaternary structures of HIV Env immunogen exhibit conformational vicissitudes and interface diminution elicited by ligand binding, Proceedings of the National Academy of Sciences, vol.128, issue.1, pp.6091-6096, 2011.
DOI : 10.1006/jsbi.1999.4174
URL : http://www.pnas.org/content/108/15/6091.full.pdf

J. B. Munro, J. Gorman, X. Ma, Z. Zhou, J. Arthos et al., Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions, Science, vol.106, issue.9, p.759, 2014.
DOI : 10.1073/pnas.0807820106

M. Naughtin, Z. Haftek-terreau, J. Xavier, S. Meyer, M. Silvain et al., DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity, PLOS ONE, vol.36, issue.11, p.129427, 2015.
DOI : 10.1371/journal.pone.0129427.s007
URL : https://hal.archives-ouvertes.fr/pasteur-01416841

D. C. Nickle, M. Rolland, M. A. Jensen, S. L. Pond, and W. Deng,

J. I. Heckerman, N. Mullins, and . Jojic, Coping with Viral Diversity in HIV Vaccine Design, PLOS Computational Biology, vol.3, issue.4, p.75, 2007.

K. E. Ocwieja, T. L. Brady, K. Ronen, A. Huegel, S. L. Roth et al.,

J. A. Towers, S. K. Young, R. Chanda, N. König, C. C. Malani et al., HIV Integration Targeting: A Pathway Involving Transportin-3 and the Nuclear Pore Protein RanBP2, PLOS Pathogens, vol.7, issue.3, p.1001313, 2011.

L. J. Parent, New insights into the nuclear localization of retroviral gag proteins, Nucleus, vol.70, issue.2, pp.92-97, 2011.
DOI : 10.1016/j.jmb.2005.04.046

M. Pasi, D. Mornico, S. Volant, A. Juchet, J. Batisse et al., DNA minicircles clarify the specific role of DNA structure on retroviral integration, Nucleic Acids Research, vol.269, issue.16, pp.7830-7847, 2016.
DOI : 10.1016/j.chom.2014.09.016
URL : https://hal.archives-ouvertes.fr/pasteur-01416869

D. O. Passos, M. Li, R. Yang, S. V. Rebensburg, R. Ghirlando et al.,

R. Kvaratskhelia, D. Craigie, and . Lyumkis, Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome, Science, vol.355, issue.6320, p.89, 2017.

K. Peng, W. Muranyi, B. Glass, V. Laketa, S. R. Yant et al., Author response, eLife, vol.9, issue.455, p.4114, 2014.
DOI : 10.7554/eLife.04114.022

E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt et al., UCSF Chimera?A visualization system for exploratory research and analysis, Journal of Computational Chemistry, vol.373, issue.13, pp.1605-1612, 2004.
DOI : 10.1038/373167a0

S. C. Pettit, M. D. Moody, R. S. Wehbie, A. H. Kaplan, P. V. Nantermet et al.,

. Swanstrom, The p2 domain of human immunodeficiency virus type 1 Gag regulates sequential proteolytic processing and is required to produce fully infectious virions, Journal of Virology, vol.68, issue.12, pp.8017-8027, 1994.

A. Piantadosi, B. Chohan, V. Chohan, R. S. Mcclelland, and J. Overbaugh, Chronic HIV-1 Infection Frequently Fails to Protect against Superinfection, PLoS Pathogens, vol.73, issue.11, p.177, 2007.
DOI : 10.1371/journal.ppat.0030177.st002

J. Plantier, M. Leoz, J. E. Dickerson, and F. De,

D. L. Damond, F. Robertson, and . Simon, A new human immunodeficiency virus derived from gorillas, Nat Med, vol.15, issue.8, pp.871-872, 2009.

E. Potterton, P. Briggs, M. Turkenburg, and E. Dodson, A graphical user interface to the CCP4 program suite, Acta Crystallogr D Biol Crystallogr, vol.59, 2003.

F. M. Poulsen, <A brief introduction to NMR spectroscopy of proteins>, 2002.

R. L. Powell, M. M. Urbanski, S. Burda, T. Kinge, and P. N. Nyambi, High Frequency of HIV-1 Dual Infections Among HIV-Positive Individuals in Cameroon, West Central Africa, JAIDS Journal of Acquired Immune Deficiency Syndromes, vol.50, issue.1, pp.84-92, 2009.
DOI : 10.1097/QAI.0b013e31818d5a40

M. M. Pradeepa, H. G. Sutherland, J. Ule, G. R. Grimes, and W. A. Bickmore, , 2012.

, Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing, PLOS Genetics, vol.8, issue.5, p.1002717

A. J. Price, A. J. Fletcher, T. Schaller, T. Elliott, K. Lee et al.,

J. Towers and L. C. James, CPSF6 Defines a Conserved Capsid Interface that Modulates HIV-1 Replication, PLOS Pathogens, vol.8, issue.8, p.1002896, 2012.

P. K. Quashie, T. Mesplède, Y. Han, M. Oliveira, D. N. Singhroy et al., Characterization of the R263K Mutation in HIV-1, 2012.

, Integrase That Confers Low-Level Resistance to the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir, Journal of Virology, vol.86, issue.5, pp.2696-2705

N. K. Raghavendra, N. Shkriabai, R. L. Graham, S. Hess, M. Kvaratskhelia et al., Identification of host proteins associated with HIV-1 preintegration complexes isolated from infected CD4+ cells, Retrovirology, vol.7, issue.1, p.66, 2010.
DOI : 10.1186/1742-4690-7-66

W. J. Rausch and F. S. Grice, HIV Rev Assembly on the Rev Response Element (RRE): A Structural Perspective, Viruses, vol.3, issue.6, 2015.
DOI : 10.1186/s12977-015-0159-3

X. Ren and J. H. Hurley, Proline-Rich Regions and Motifs in Trafficking: From ESCRT Interaction to Viral Exploitation, Traffic, vol.3, issue.10, pp.12-1282, 2011.
DOI : 10.1021/cb800193n

C. D. Rizzuto, R. Wyatt, N. Hernández-ramos, Y. Sun, P. D. Kwong et al., A Conserved HIV gp120 Glycoprotein Structure Involved in Chemokine Receptor Binding, Conserved HIV gp120 Glycoprotein Structure Involved in Chemokine Receptor Binding, p.1949, 1998.
DOI : 10.1126/science.280.5371.1949

P. E. Sax, J. L. Meyers, M. Mugavero, and K. L. Davis, Adherence to Antiretroviral Treatment and Correlation with Risk of Hospitalization among Commercially Insured HIV Patients in the United States, PLoS ONE, vol.28, issue.2, p.31591, 2012.
DOI : 10.1371/journal.pone.0031591.t005

A. R. Schröder, P. Shinn, H. Chen, C. Berry, J. R. Ecker et al., , 2002.

, Integration in the Human Genome Favors Active Genes and Local Hotspots, Cell, vol.110, issue.4, pp.521-529

C. D. Schwieters, J. J. Kuszewski, N. Tjandra, and G. M. Clore, The Xplor-NIH NMR molecular structure determination package, Journal of Magnetic Resonance, vol.160, issue.1, pp.65-73, 2003.
DOI : 10.1016/S1090-7807(02)00014-9

S. A. Seidel, P. M. Dijkman, W. A. Lea, G. Van-den, and . Bogaart,

J. S. Lazic, P. Joseph, P. Srinivasan, A. Baaske, I. Simeonov et al.,

G. Ladbury, A. Schreiber, D. Watts, S. Braun, and . Duhr, Microscale Thermophoresis Quantifies Biomolecular Interactions under Previously Challenging Conditions, Methods, vol.59, issue.3, pp.301-315, 2013.

E. Serrao, L. Krishnan, M. Shun, X. Li, P. Cherepanov et al., Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: implications for the mechanism of target DNA binding, Nucleic Acids Research, vol.269, issue.8, pp.5164-5176, 2014.
DOI : 10.1073/pnas.91.13.5913

A. Sharma, R. C. Larue, M. R. Plumb, N. Malani, F. Male et al., J. J. Kessl, N

E. Shkriabai, S. S. Coward, P. L. Aiyer, L. Green, M. J. Wu et al.,

, BET proteins promote efficient murine leukemia virus integration at transcription start sites, Kvaratskhelia Proceedings of the National Academy of Sciences of the United States of America, vol.110, issue.29, pp.12036-12041, 2013.

P. M. Sharp and B. H. Hahn, Origins of HIV and the AIDS Pandemic, Cold Spring Harbor Perspectives in Medicine, vol.1, issue.1, p.6841, 2011.
DOI : 10.1101/cshperspect.a006841
URL : http://perspectivesinmedicine.cshlp.org/content/1/1/a006841.full.pdf

G. M. Shaw and E. Hunter, HIV Transmission, Cold Spring Harbor Perspectives in Medicine, vol.2, issue.11, p.6965, 2012.
DOI : 10.1101/cshperspect.a006965

M. Shun, Y. Botbol, X. Li, F. Di-nunzio, J. E. Daigle et al., Identification and Characterization of PWWP Domain Residues Critical for LEDGF/p75 Chromatin Binding and Human Immunodeficiency Virus Type 1 Infectivity, Journal of Virology, vol.82, issue.23, 2008.
DOI : 10.1128/JVI.01561-08
URL : https://hal.archives-ouvertes.fr/pasteur-01536189

. Infectivity, Journal of Virology, vol.82, issue.23, pp.11555-11567

M. C. Shun, N. K. Raghavendra, N. Vandegraaff, J. E. Daigle, S. Hughes et al., LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration, Genes & Development, vol.21, issue.14, 2007.
DOI : 10.1101/gad.1565107
URL : http://genesdev.cshlp.org/content/21/14/1767.full.pdf

E. Simon-loriere, D. P. Martin, K. M. Weeks, and M. Negroni, RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1, Journal of Virology, vol.84, issue.24, pp.12675-12682, 2010.
DOI : 10.1128/JVI.01302-10
URL : https://hal.archives-ouvertes.fr/hal-00530063

R. D. Sloan and M. A. Wainberg, The role of unintegrated DNA in HIV infection, Retrovirology, vol.8, issue.1, p.52, 2011.
DOI : 10.1073/pnas.86.15.5743

N. Sluis-cremer, M. A. Wainberg, and R. F. Schinazi, Resistance to reverse transcriptase inhibitors used in the treatment and prevention of HIV-1 infection, Future Microbiology, vol.39, issue.11, pp.1773-1782, 2015.
DOI : 10.1128/AAC.02729-14

R. P. Smyth, T. E. Schlub, A. J. Grimm, C. Waugh, and P. ,

J. Cromer, M. P. Mak, and . Davenport, Identifying Recombination Hot Spots in the HIV-1 Genome, Journal of Virology, vol.88, issue.5, pp.2891-2902, 2014.

G. A. Sowd, E. Serrao, H. Wang, W. Wang, H. J. Fadel et al., A critical role for alternative polyadenylation factor CPSF6 in targeting HIV-1 integration to transcriptionally active chromatin, Proceedings of the National Academy of Sciences, vol.70, issue.2, pp.1054-1063, 2016.
DOI : 10.1093/nar/gkt074

D. Ssemwanga, R. N. Nsubuga, B. N. Mayanja, F. Lyagoba, B. Magambo et al., Effect of HIV-1 Subtypes on Disease Progression in Rural Uganda: A Prospective Clinical Cohort Study, PLoS ONE, vol.22, issue.8, p.71768, 2013.
DOI : 10.1371/journal.pone.0071768.t004

K. E. Stephenson, H. T. Couto, and D. H. Barouch, , 2016.

, vaccine development, Current Opinion in Immunology, vol.41, pp.39-46

F. Turlure, G. Maertens, S. Rahman, P. Cherepanov, and A. Engelman, A tripartite DNA-binding element, comprised of the nuclear localization signal and two AT-hook motifs, mediates the association of LEDGF/p75 with chromatin in vivo, Nucleic Acids Research, vol.34, issue.5, pp.1653-1665, 2006.
DOI : 10.1093/nar/gkl052

A. Vagin and A. Teplyakov, Molecular replacement with MOLREP, Acta Crystallogr D Biol Crystallogr, vol.66, 2010.

F. Van-heuverswyn, Y. Li, C. Neel, E. Bailes, B. F. Keele et al.,

Y. Liegeois, E. M. Bienvenue, P. M. Ngolle, G. M. Sharp, E. Shaw et al., Human immunodeficiency viruses: SIV infection in wild gorillas, Nature, vol.444, issue.7116, pp.164-164, 2006.

R. Van-nuland, F. M. Van-schaik, M. Simonis, and S. Van,

M. Timmers and H. Van-ingen, Nucleosomal DNA binding drives the recognition of H3K36-methylated nucleosomes by the PSIP1-PWWP domain, Epigenetics & Chromatin, vol.6, pp.12-12, 2013.

G. C. Van-zundert, J. P. Rodrigues, M. Trellet, and C. ,

A. S. Karaca, M. Melquiond, S. J. Van-dijk, A. M. De-vries, and . Bonvin, The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes, Journal of Molecular Biology, vol.428, issue.4, pp.720-725, 2016.

W. F. Vranken, W. Boucher, T. J. Stevens, R. H. Fogh, A. Pajon et al.,

J. Markley, E. D. Ionides, and . Laue, The CCPN data model for NMR spectroscopy: Development of a software pipeline, Proteins: Structure, Function, and Bioinformatics, vol.59, issue.4, pp.687-696, 2005.

W. H. Wang, D. , W. Lu, and F. Li, Pharmacological intervention of HIV-1 maturation, Acta Pharmaceutica Sinica B, vol.5, issue.6, pp.493-499, 2015.
DOI : 10.1016/j.apsb.2015.05.004

J. Wang, H. Ling, W. Yang, and R. Craigie, Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein, The EMBO Journal, vol.20, issue.24, pp.7333-7343, 2001.
DOI : 10.1093/emboj/20.24.7333

J. M. Watts, K. K. Dang, R. J. Gorelick, C. W. Leonard, J. W. Bess et al., Architecture and secondary structure of an entire HIV-1, 2009.

R. Genome, Nature, vol.460, issue.7256, pp.711-716

Z. Weng, R. J. Rickles, S. Feng, S. Richard, A. S. Shaw et al., Structure-function analysis of SH3 domains: SH3 binding specificity altered by single amino acid substitutions., Molecular and Cellular Biology, vol.15, issue.10, pp.5627-5634, 1995.
DOI : 10.1128/MCB.15.10.5627

J. O. Wertheim and M. Worobey, Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2, PLoS Computational Biology, vol.77, issue.5, p.1000377, 2009.
DOI : 10.1371/journal.pcbi.1000377.s009

M. P. Williamson, Using chemical shift perturbation to characterise ligand binding, Progress in Nuclear Magnetic Resonance Spectroscopy, vol.73, pp.1-16, 2013.
DOI : 10.1016/j.pnmrs.2013.02.001

A. Wlodawer, W. Minor, Z. Dauter, and M. Jaskolski, Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures, FEBS Journal, vol.40, issue.1, pp.1-21, 2008.
DOI : 10.1021/bi011817n

N. Yan, E. O. Day, L. A. Wheeler, A. Engelman, and J. Lieberman, HIV DNA is heavily uracilated, which protects it from autointegration, Proceedings of the National Academy of Sciences, vol.26, issue.11, pp.9244-9249, 2011.
DOI : 10.1146/annurev.immunol.26.021607.090404

K. L. Yap and M. Zhou, Keeping it in the family: diverse histone recognition by conserved structural folds, Critical Reviews in Biochemistry and Molecular Biology, vol.282, issue.6, pp.488-505, 2010.
DOI : 10.1074/jbc.M604029200

K. E. Yoder and F. D. Bushman, Repair of Gaps in Retroviral DNA Integration Intermediates, Journal of Virology, vol.74, issue.23, pp.11191-11200, 2000.
DOI : 10.1128/JVI.74.23.11191-11200.2000
URL : http://jvi.asm.org/content/74/23/11191.full.pdf

R. Zheng, T. M. Jenkins, and R. Craigie, Zinc folds the N-terminal domain of HIV-1, 1996.
DOI : 10.1073/pnas.93.24.13659
URL : http://www.pnas.org/content/93/24/13659.full.pdf

, integrase, promotes multimerization, and enhances catalytic activity, Proceedings of the National Academy of Sciences of the United States of America, vol.93, issue.24, pp.13659-13664

C. Zhou and T. M. Rana, A Bimolecular Mechanism of HIV-1 Tat Protein Interaction with RNA Polymerase II Transcription Elongation Complexes, Journal of Molecular Biology, vol.320, issue.5, pp.925-942, 2002.
DOI : 10.1016/S0022-2836(02)00556-9

J. J. Ziarek, F. C. Peterson, B. L. Lytle, and B. F. Volkman, Binding Site Identification and Structure Determination of Protein???Ligand Complexes by NMR, Methods in enzymology, vol.493, pp.241-275, 2011.
DOI : 10.1016/B978-0-12-381274-2.00010-8