Human immunodeficiency virus (HIV) has a small genome and therefore relies heavily on the host cellular machinery to replicate. Identifying which host proteins and complexes come into physical contact with the viral proteins is crucial for a comprehensive understanding of how HIV rewires the host’s cellular machinery during the course of infection. Here we report the use of affinity tagging and purification mass spectrometry1,2,3 to determine systematically the physical interactions of all 18 HIV-1 proteins and polyproteins with host proteins in two different human cell lines (HEK293 and Jurkat). Using a quantitative scoring system that we call MiST, we identified with high confidence 497 HIV–human protein–protein interactions involving 435 individual human proteins, with 40% of the interactions being identified in both cell types. We found that the host proteins hijacked by HIV, especially those found interacting in both cell types, are highly conserved across primates. We uncovered a number of host complexes targeted by viral proteins, including the finding that HIV protease cleaves eIF3d, a subunit of eukaryotic translation initiation factor 3. This host protein is one of eleven identified in this analysis that act to inhibit HIV replication. This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636 (2006)

  2. 2.

    et al. Purification and characterization of HIV-human protein complexes. Methods 53, 13–19 (2011)

  3. 3.

    et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637–643 (2006)

  4. 4.

    , , & Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389–403 (2009)

  5. 5.

    et al. High-quality binary protein interaction map of the yeast interactome network. Science 322, 104–110 (2008)

  6. 6.

    et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957–968 (2005)

  7. 7.

    et al. An in vivo map of the yeast protein interactome. Science 320, 1465–1470 (2008)

  8. 8.

    et al. Epstein-Barr virus and virus human protein interaction maps. Proc. Natl Acad. Sci. USA 104, 7606–7611 (2007)

  9. 9.

    et al. A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139, 1255–1267 (2009)

  10. 10.

    et al. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics 6, 439–450 (2007)

  11. 11.

    et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nature Methods 8, 70–73 (2011)

  12. 12.

    & HIV-1 accessory proteins–ensuring viral survival in a hostile environment. Cell Host Microbe 3, 388–398 (2008)

  13. 13.

    et al. The structural basis for 14-3-3:phosphopeptide binding specificity. Cell 91, 961–971 (1997)

  14. 14.

    et al. VirusMINT: a viral protein interaction database. Nucleic Acids Res. 37, D669–D673 (2009)

  15. 15.

    et al. Identification of host proteins required for HIV infection through a functional genomic screen. Science 319, 921–926 (2008)

  16. 16.

    et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135, 49–60 (2008)

  17. 17.

    , , & A genome-wide short hairpin RNA screening of Jurkat T-cells for human proteins contributing to productive HIV-1 replication. J. Biol. Chem. 284, 19463–19473 (2009)

  18. 18.

    et al. Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 4, 495–504 (2008)

  19. 19.

    et al. CORUM: the comprehensive resource of mammalian protein complexes–2009. Nucleic Acids Res. 38, D497–D501 (2010)

  20. 20.

    et al. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 34, D535–D539 (2006)

  21. 21.

    et al. GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. BMC Bioinformatics 12, 298 (2011)

  22. 22.

    eIF3: a versatile scaffold for translation initiation complexes. Trends Biochem. Sci. 31, 553–562 (2006)

  23. 23.

    , , & HIV protease cleaves poly(A)-binding protein. Biochem. J. 396, 219–226 (2006)

  24. 24.

    et al. Apoptosis mediated by HIV protease is preceded by cleavage of Bcl-2. Proc. Natl Acad. Sci. USA 93, 9571–9576 (1996)

  25. 25.

    & Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nature Biotechnol. 26, 685–694 (2008)

  26. 26.

    et al. Structure of cDNAs encoding human eukaryotic initiation factor 3 subunits. Possible roles in RNA binding and macromolecular assembly. J. Biol. Chem. 272, 27042–27052 (1997)

  27. 27.

    , , , & Inhibition of HIV-1 replication by eIF3f. Proc. Natl Acad. Sci. USA 106, 4071–4078 (2009)

  28. 28.

    et al. Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection. Nature http://dx.doi.org/10.1038/nature10693 (this issue).

  29. 29.

    et al. Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. Proc. Natl Acad. Sci. USA 105, 18139–18144 (2008)

Download references


We thank A. Choi, Z. Rizvi and E. Kwon for cloning of human genes and J. Cate for purified eIF3. We also thank J. Gross, R. Andino, R. Harris, M. Daugherty and members of the Krogan lab for discussion. This research was funded by grants from QB3@UCSF and the National Institutes of Health (P50 GM082250 to N.J.K., A.D.F., C.S.C. and T.A.; P01 AI090935 to N.J.K., S.K.C., J.A.Y. and F.D.B.; P50 GM081879 to N.J.K. and A.B.; P50 GM082545 to W.I.S.; P41RR001614 to A.B.; U54 RR022220 to A.S.; P01 GM073732-05 to A.T.; CHRP-ID08-TBI-063 to S.K.C.; P41 RR001081 to J.H.M.) and from the Nomis Foundation (to J.A.Y.). N.J.K. is a Searle Scholar and a Keck Young Investigator.

Author information

Author notes

    • Iván D’Orso

    Present address: Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA, 75390


  1. Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA

    • Stefanie Jäger
    • , Natali Gulbahce
    • , Jeffrey R. Johnson
    • , Kathryn E. McGovern
    • , Michael Shales
    • , Kathy Li
    • , Hilda Hernandez
    • , Gwendolyn M. Jang
    • , Marie Fahey
    • , Cathal Mahon
    •  & Nevan J. Krogan
  2. California Institute for Quantitative Biosciences, QB3, San Francisco, California 94158, USA

    • Stefanie Jäger
    • , Peter Cimermancic
    • , Natali Gulbahce
    • , Jeffrey R. Johnson
    • , Kathryn E. McGovern
    • , Michael Shales
    • , Kathy Li
    • , Hilda Hernandez
    • , Gwendolyn M. Jang
    • , Eyal Akiva
    • , Marie Fahey
    • , Cathal Mahon
    • , Tanja Kortemme
    • , Ryan D. Hernandez
    • , Charles S. Craik
    • , Alma Burlingame
    • , Andrej Sali
    • , Alan D. Frankel
    •  & Nevan J. Krogan
  3. Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA

    • Peter Cimermancic
    • , Eyal Akiva
    • , Tanja Kortemme
    • , Ryan D. Hernandez
    •  & Andrej Sali
  4. J. David Gladstone Institutes, San Francisco, California 94158, USA

    • Jeffrey R. Johnson
    •  & Nevan J. Krogan
  5. Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA

    • Starlynn C. Clarke
    • , Kathy Li
    • , Hilda Hernandez
    • , Cathal Mahon
    • , Anthony J. O’Donoghue
    • , John H. Morris
    • , David A. Maltby
    • , Charles S. Craik
    • , Alma Burlingame
    •  & Andrej Sali
  6. Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA

    • Gaelle Mercenne
    •  & Wesley I. Sundquist
  7. Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA

    • Lars Pache
    •  & Sumit K. Chanda
  8. Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA

    • Gwendolyn M. Jang
    • , Iván D’Orso
    • , Jason Fernandes
    •  & Alan D. Frankel
  9. Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

    • Shoshannah L. Roth
    • , Melanie Stephens
    •  & Frederic D. Bushman
  10. The Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • John Marlett
    •  & John A. Young
  11. Department of Chemistry, University of California, Berkeley, California 94720, USA

    • Aleksandar Todorovic
  12. Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA

    • Tom Alber
  13. Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

    • Gerard Cagney
  14. Host Pathogen Circuitry Group, University of California, San Francisco, California 94158, USA

    • Tanja Kortemme
    • , Ryan D. Hernandez
    • , Andrej Sali
    • , Alan D. Frankel
    •  & Nevan J. Krogan


  1. Search for Stefanie Jäger in:

  2. Search for Peter Cimermancic in:

  3. Search for Natali Gulbahce in:

  4. Search for Jeffrey R. Johnson in:

  5. Search for Kathryn E. McGovern in:

  6. Search for Starlynn C. Clarke in:

  7. Search for Michael Shales in:

  8. Search for Gaelle Mercenne in:

  9. Search for Lars Pache in:

  10. Search for Kathy Li in:

  11. Search for Hilda Hernandez in:

  12. Search for Gwendolyn M. Jang in:

  13. Search for Shoshannah L. Roth in:

  14. Search for Eyal Akiva in:

  15. Search for John Marlett in:

  16. Search for Melanie Stephens in:

  17. Search for Iván D’Orso in:

  18. Search for Jason Fernandes in:

  19. Search for Marie Fahey in:

  20. Search for Cathal Mahon in:

  21. Search for Anthony J. O’Donoghue in:

  22. Search for Aleksandar Todorovic in:

  23. Search for John H. Morris in:

  24. Search for David A. Maltby in:

  25. Search for Tom Alber in:

  26. Search for Gerard Cagney in:

  27. Search for Frederic D. Bushman in:

  28. Search for John A. Young in:

  29. Search for Sumit K. Chanda in:

  30. Search for Wesley I. Sundquist in:

  31. Search for Tanja Kortemme in:

  32. Search for Ryan D. Hernandez in:

  33. Search for Charles S. Craik in:

  34. Search for Alma Burlingame in:

  35. Search for Andrej Sali in:

  36. Search for Alan D. Frankel in:

  37. Search for Nevan J. Krogan in:


S.J. generated the protein–protein interaction map; P.C. developed the MiST scoring system; N.G., M. Shales, E.A., M.F., J.H.M., J.R.J. and R.D.H. provided computational support; K.E.M., K.L., J.R.J., H.H., G.M.J., I.D., J.F. and D.A.M. provided experimental support; S.J., S.C.C., A.J.O. and A.T. characterized the PR–eIF3d interaction; S.J., G.M.J., C.M. and G.M. confirmed the interactions by immunoprecipitation/western blot; L.P., S.L.R., J.M. and M. Stephens used RNAi for functional verification; T.A., G.C., F.D.B., J.A.Y., S.K.C., W.I.S., T.K., R.D.H., C.S.C., A.B., A.S., A.D.F. and N.J.K. supervised the research; and S.J., P.C., A.S. and N.J.K. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nevan J. Krogan.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    The file contains Supplementary Figures 1-20 with legends, Supplementary Tables 1-14, Supplementary Methods, a Supplementary Discussion and Supplementary References.

Excel files

  1. 1.

    Supplementary Data 1

    The data shows raw MS data.

  2. 2.

    Supplementary Data 2

    The data shows three components used for MiST scoring.

  3. 3.

    Supplementary Data 3

    The data shows MiST scored MS data (>0.75 and full list).

  4. 4.

    Supplementary Data 4

    The data shows functional enrichment of host factors.

  5. 5.

    Supplementary Data 5

    The data shows VirusMint PPIs.

  6. 6.

    Supplementary Data 6

    The data shows overlap of VirusMint with all MiST scores.

  7. 7.

    Supplementary Data 7

    The data shows published RNAi screens.

  8. 8.

    Supplementary Data 8

    The data shows overlap of RNAi screens with all MiST scores.

  9. 9.

    Supplementary Data 9

    The data shows human-human PPIs used in HIV-human network representation.

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.