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For Proteins, Form Shapes Function

Structure of HIV

An illustration of the structure of HIV, with identified proteins labeled. Credit: David S. Goodsell, RCSB PDB http://www.pdb.org IN PR MA CA SU and TM NC Tat Rev Nef P6 Vpr Vif Vpu RT
An illustration of the structure of HIV, with identified proteins labeled. Credit: David S. Goodsell, RCSB PDB. http://www.pdb.org Link to external Web site. Click on any labeled protein in the image to see a description. Also, explore an interactive protein model Link to external Web site.

Structural Proteins

  • MA
    Matrix protein
    PDB entry 1hiw
    C. P. Hill, D. Worthylake, D. P. Bancroft, A. M. Christensen, W. I. Sundquist. (1996) Crystal structures of the trimeric human immunodeficiency virus type 1 matrix protein: implications for membrane association and assembly. Proc Natl Acad Sci U S A 93: 3099-3104.
  • CA
    Capsid protein
    PDB entry 3h47.
    O. Pornillos, B. K. Ganser-Pornillos, B. N. Kelly, Y. Hua, F. G. Whitby, C. D. Stout, W. I. Sundquist, C. P. Hill, M. Yeager. (2009) X-ray structures of the hexameric building block of the HIV capsid. Cell 137: 1282-1292.
  • NC
    Nucleocapsid protein
    PDB entry 1a1t.
    R. N. De Guzman, Z. R. Wu, C. C. Stalling, L. Pappalardo, P. N. Borer, M. F. Summers. (1998) Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element. Science 279: 384-388.
  • SU and TM
    Envelope proteins
    PDB entries 2ezo and 1g9m.
    M. Caffrey, M. Cai, J. Kaufman, S. J. Stahl, P. T. Wingfield, D. G. Covell, A. M. Gronenborn, G. M. Clore. (1998) Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41. EMBO J 17: 4572-4584.
    P. D. Kwong, R. Wyatt, S. Majeed, J. Robinson, R. W. Sweet, J. Sodroski, W. A. Hendrickson. (2000) Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure 8: 1329-1339.

Viral Enzymes

  • RT
    Reverse transcriptase
    PDB entry 1hys.
    S. G. Sarafianos, K. Das, C. Tantillo, A. D. Clark Jr., J. Ding, J. Whitcomb, P. L. Boyer, S. H. Hughes, E. Arnold. (2001) Crystal structre of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. EMBO J. 20: 1449-1461.
  • IN
    Integrase
    PDB entry 1ex4.
    J. C. Chen, J. Krucinski, L. J. Miercke, J. S. Finer-Moore, A. H. Tang, A. D. Leavitt, R. M. Stroud. (2000) Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding. Proc Natl Acad Sci U S A 97: 8233-8238.
  • PR
    HIV protease
    PDB entry 1hpv.
    E. E. Kim, C. T. Baker, M. D. Dwyer, M. A. Murcko, B. G. Rao, R. D. Tung, M. A. Navia. (1995) Crystal Structure of HIV-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme. J.Am.Chem.Soc. 117: 1181-1182.

Accessory Proteins

  • Tat
    Tat (trans-activator of transcription) PDB entries 1biv and 1jfw.
    X. Ye, R. A. Kumar, D. J. Patel. (1995) Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex. Chem Biol 2: 827-840.
    J. M. Peloponese, Jr., C. Gregoire, S. Opi, D. Esquieu, J. Sturgis, E. Lebrun, E. Meurs, Y. Collette, D. Olive, A. M. Aubertin, M. Witvrow, C. Pannecouque, E. De Clercq, C. Bailly, J. Lebreton, E. P. Loret. (2000) 1H-13C nuclear magnetic resonance assignment and structural characterization of HIV-1 Tat protein. C R Acad Sci III 323: 883-894.
  • Rev
    Rev (regulator of virion)
    PDB entry 1etf.
    J. L. Battiste, H. Mao, N. S. Rao, R. Tan, D. R. Muhandiram, L. E. Kay, A. D. Frankel, J. R. Williamson. (1996) Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex. Science 273: 1547-1551.
  • Vif
    Vif (viral infectivity factor)
    PDB entry 3dcg.
    B. J. Stanley, E. S. Ehrlich, L. Short, Y. Yu, Z. Xiao, X. F. Yu, Y. Xiong. (2008) Structural insight into the human immunodeficiency virus Vif SOCS box and its role in human E3 ubiquitin ligase assembly. J Virol 82: 8656-8663.
  • Vpu
    Vpu (viral protein u)
    PDB entries 1pi7 and 1vpu.
    S. H. Park, A. A. Mrse, A. A. Nevzorov, M. F. Mesleh, M. Oblatt-Montal, M. Montal, S. J. Opella. (2003) Three-dimensional structure of the channel-forming trans-membrane domain of virus protein "u" (Vpu) from HIV-1. J Mol Biol 333: 409-424.
    D. Willbold, S. Hoffmann, P. Rosch. (1997) Secondary structure and tertiary fold of the human immunodeficiency virus protein U (Vpu) cytoplasmic domain in solution. Eur J Biochem 245: 581-588.
  • Vpr
    Vpr (viral protein r)
    PDB entry 1esx.
    K. Wecker, N. Morellet, S. Bouaziz, B. P. Roques. (2002) NMR structure of the HIV-1 regulatory protein Vpr in H2O/trifluoroethanol. Comparison with the Vpr N-terminal (1-51) and C-terminal (52-96) domains. Eur J Biochem 269: 3779-3788.
  • Nef
    Nef (negative regulatory factor)
    PDB entries 1avv and 1qa5.
    S. Arold, P. Franken, M. P. Strub, F. Hoh, S. Benichou, R. Benarous, C. Dumas. (1997) The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling. Structure 5: 1361-1372.
    M. Geyer, C. E. Munte, J. Schorr, R. Kellner, H. R. Kalbitzer. (1999) Structure of the anchor-domain of myristoylated and non-myristoylated HIV-1 Nef protein. J Mol Biol 289: 123-138.
  • P6
    Currently there is no structure for it in the PDB.

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This page last reviewed on May 5, 2011