Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G

Abstract

The human APOBEC3G (A3G) DNA cytosine deaminase restricts and hypermutates DNA-based parasites including HIV-1. The viral infectivity factor (Vif) prevents restriction by triggering A3G degradation. Although the structure of the A3G catalytic domain is known, the structure of the N-terminal Vif-binding domain has proven more elusive. Here, we used evolution- and structure-guided mutagenesis to solubilize the Vif-binding domain of A3G, thus permitting structural determination by NMR spectroscopy. A smaller zinc-coordinating pocket and altered helical packing distinguish the structure from previous catalytic-domain structures and help to explain the reported inactivity of this domain. This soluble A3G N-terminal domain is bound by Vif; this enabled mutagenesis and biochemical experiments, which identified a unique Vif-interacting surface formed by the α1-β1, β2-α2 and β4-α4 loops. This structure sheds new light on the Vif-A3G interaction and provides critical information for future drug development.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Generation of soluble N-terminal Vif-binding domain of A3G.
Figure 2: Solution structure of the Vif-binding domain of A3G.
Figure 3: Structure comparison of sNTD with other APOBEC3 proteins.
Figure 4: Functional assays of sNTD.
Figure 5: Identification of Vif-binding regions of sNTD.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

NCBI Reference Sequence

Protein Data Bank

References

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

    Article  CAS  Google Scholar 

  2. Harris, R.S., Hultquist, J.F. & Evans, D.T. The restriction factors of human immunodeficiency virus. J. Biol. Chem. 287, 40875–40883 (2012).

    Article  CAS  Google Scholar 

  3. Malim, M.H. & Bieniasz, P.D. HIV restriction factors and mechanisms of evasion. Cold Spring Harb. Perspect. Med. 2, a006940 (2012).

    Article  Google Scholar 

  4. Refsland, E.W. et al. Quantitative profiling of the full APOBEC3 mRNA repertoire in lymphocytes and tissues: implications for HIV-1 restriction. Nucleic Acids Res. 38, 4274–4284 (2010).

    Article  CAS  Google Scholar 

  5. Refsland, E.W., Hultquist, J.F. & Harris, R.S. Endogenous origins of HIV-1 G-to-A hypermutation and restriction in the nonpermissive T cell line CEM2n. PLoS Pathog. 8, e1002800 (2012).

    Article  CAS  Google Scholar 

  6. Ooms, M. et al. HIV-1 Vif adaptation to human APOBEC3H haplotypes. Cell Host Microbe 14, 411–421 (2013).

    Article  CAS  Google Scholar 

  7. Sato, K. et al. APOBEC3D and APOBEC3F potently promote HIV-1 diversification and evolution in humanized mouse model. PLoS Pathog. 10, e1004453 (2014).

    Article  Google Scholar 

  8. Haché, G., Liddament, M.T. & Harris, R.S. The retroviral hypermutation specificity of APOBEC3F and APOBEC3G is governed by the C-terminal DNA cytosine deaminase domain. J. Biol. Chem. 280, 10920–10924 (2005).

    Article  Google Scholar 

  9. Navarro, F. et al. Complementary function of the two catalytic domains of APOBEC3G. Virology 333, 374–386 (2005).

    Article  CAS  Google Scholar 

  10. Rathore, A. et al. The local dinucleotide preference of APOBEC3G can be altered from 5′-CC to 5′-TC by a single amino acid substitution. J. Mol. Biol. 425, 4442–4454 (2013).

    Article  CAS  Google Scholar 

  11. Harjes, S. et al. Impact of H216 on the DNA binding and catalytic activities of the HIV restriction factor APOBEC3G. J. Virol. 87, 7008–7014 (2013).

    Article  CAS  Google Scholar 

  12. Furukawa, A. et al. Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G. EMBO J. 28, 440–451 (2009).

    Article  CAS  Google Scholar 

  13. Khan, M.A. et al. Analysis of the contribution of cellular and viral RNA to the packaging of APOBEC3G into HIV-1 virions. Retrovirology 4, 48 (2007).

    Article  Google Scholar 

  14. Burnett, A. & Spearman, P. APOBEC3G multimers are recruited to the plasma membrane for packaging into human immunodeficiency virus type 1 virus-like particles in an RNA-dependent process requiring the NC basic linker. J. Virol. 81, 5000–5013 (2007).

    Article  CAS  Google Scholar 

  15. Svarovskaia, E.S. et al. Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) is incorporated into HIV-1 virions through interactions with viral and nonviral RNAs. J. Biol. Chem. 279, 35822–35828 (2004).

    Article  CAS  Google Scholar 

  16. Zennou, V., Perez-Caballero, D., Gottlinger, H. & Bieniasz, P.D. APOBEC3G incorporation into human immunodeficiency virus type 1 particles. J. Virol. 78, 12058–12061 (2004).

    Article  CAS  Google Scholar 

  17. Douaisi, M. et al. HIV-1 and MLV Gag proteins are sufficient to recruit APOBEC3G into virus-like particles. Biochem. Biophys. Res. Commun. 321, 566–573 (2004).

    Article  CAS  Google Scholar 

  18. Desimmie, B.A. et al. Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all. J. Mol. Biol. 426, 1220–1245 (2014).

    Article  CAS  Google Scholar 

  19. Feng, Y., Baig, T.T., Love, R.P. & Chelico, L. Suppression of APOBEC3-mediated restriction of HIV-1 by Vif. Front. Microbiol. 5, 450 (2014).

    Article  Google Scholar 

  20. Jäger, S. et al. Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection. Nature 481, 371–375 (2012).

    Article  Google Scholar 

  21. Zhang, W., Du, J., Evans, S.L., Yu, Y. & Yu, X.F. T-cell differentiation factor CBF-β regulates HIV-1 Vif-mediated evasion of host restriction. Nature 481, 376–379 (2012).

    Article  CAS  Google Scholar 

  22. Kao, S. et al. The human immunodeficiency virus type 1 Vif protein reduces intracellular expression and inhibits packaging of APOBEC3G (CEM15), a cellular inhibitor of virus infectivity. J. Virol. 77, 11398–11407 (2003).

    Article  CAS  Google Scholar 

  23. Marin, M., Rose, K.M., Kozak, S.L. & Kabat, D. HIV-1 Vif protein binds the editing enzyme APOBEC3G and induces its degradation. Nat. Med. 9, 1398–1403 (2003).

    Article  CAS  Google Scholar 

  24. Sheehy, A.M., Gaddis, N.C. & Malim, M.H. The antiretroviral enzyme APOBEC3G is degraded by the proteasome in response to HIV-1 Vif. Nat. Med. 9, 1404–1407 (2003).

    Article  CAS  Google Scholar 

  25. Conticello, S.G., Harris, R.S. & Neuberger, M.S. The Vif protein of HIV triggers degradation of the human antiretroviral DNA deaminase APOBEC3G. Curr. Biol. 13, 2009–2013 (2003).

    Article  CAS  Google Scholar 

  26. Russell, R.A. & Pathak, V.K. Identification of two distinct human immunodeficiency virus type 1 Vif determinants critical for interactions with human APOBEC3G and APOBEC3F. J. Virol. 81, 8201–8210 (2007).

    Article  CAS  Google Scholar 

  27. Pery, E., Rajendran, K.S., Brazier, A.J. & Gabuzda, D. Regulation of APOBEC3 proteins by a novel YXXL motif in human immunodeficiency virus type 1 Vif and simian immunodeficiency virus SIVagm Vif. J. Virol. 83, 2374–2381 (2009).

    Article  CAS  Google Scholar 

  28. Chen, G., He, Z., Wang, T., Xu, R. & Yu, X.F. A patch of positively charged amino acids surrounding the human immunodeficiency virus type 1 Vif SLVx4Yx9Y motif influences its interaction with APOBEC3G. J. Virol. 83, 8674–8682 (2009).

    Article  CAS  Google Scholar 

  29. Dang, Y., Wang, X., Zhou, T., York, I.A. & Zheng, Y.H. Identification of a novel WxSLVK motif in the N terminus of human immunodeficiency virus and simian immunodeficiency virus Vif that is critical for APOBEC3G and APOBEC3F neutralization. J. Virol. 83, 8544–8552 (2009).

    Article  CAS  Google Scholar 

  30. Guo, Y. et al. Structural basis for hijacking CBF-β and CUL5 E3 ligase complex by HIV-1 Vif. Nature 505, 229–233 (2014).

    Article  CAS  Google Scholar 

  31. Chen, K.M. et al. Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G. Nature 452, 116–119 (2008).

    Article  CAS  Google Scholar 

  32. Harjes, E. et al. An extended structure of the APOBEC3G catalytic domain suggests a unique holoenzyme model. J. Mol. Biol. 389, 819–832 (2009).

    Article  CAS  Google Scholar 

  33. Holden, L.G. et al. Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications. Nature 456, 121–124 (2008).

    Article  CAS  Google Scholar 

  34. Shandilya, S.M. et al. Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces. Structure 18, 28–38 (2010).

    Article  CAS  Google Scholar 

  35. Bohn, M.F. et al. Crystal structure of the DNA cytosine deaminase APOBEC3F: the catalytically active and HIV-1 Vif-binding domain. Structure 21, 1042–1050 (2013).

    Article  CAS  Google Scholar 

  36. Siu, K.K., Sultana, A., Azimi, F.C. & Lee, J.E. Structural determinants of HIV-1 Vif susceptibility and DNA binding in APOBEC3F. Nat. Commun. 4, 2593 (2013).

    Article  Google Scholar 

  37. Byeon, I.J. et al. NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity. Nat. Commun. 4, 1890 (2013).

    Article  Google Scholar 

  38. Kitamura, S. et al. The APOBEC3C crystal structure and the interface for HIV-1 Vif binding. Nat. Struct. Mol. Biol. 19, 1005–1010 (2012).

    Article  CAS  Google Scholar 

  39. LaRue, R.S. et al. Guidelines for naming nonprimate APOBEC3 genes and proteins. J. Virol. 83, 494–497 (2009).

    Article  CAS  Google Scholar 

  40. Salzmann, M., Pervushin, K., Wider, G., Senn, H. & Wuthrich, K. TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc. Natl. Acad. Sci. USA 95, 13585–13590 (1998).

    Article  CAS  Google Scholar 

  41. Pervushin, K., Riek, R., Wider, G. & Wuthrich, K. Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad. Sci. USA 94, 12366–12371 (1997).

    Article  CAS  Google Scholar 

  42. Newman, E.N. et al. Antiviral function of APOBEC3G can be dissociated from cytidine deaminase activity. Curr. Biol. 15, 166–170 (2005).

    Article  CAS  Google Scholar 

  43. Russell, R.A., Smith, J., Barr, R., Bhattacharyya, D. & Pathak, V.K. Distinct domains within APOBEC3G and APOBEC3F interact with separate regions of human immunodeficiency virus type 1 Vif. J. Virol. 83, 1992–2003 (2009).

    Article  CAS  Google Scholar 

  44. Bogerd, H.P., Doehle, B.P., Wiegand, H.L. & Cullen, B.R. A single amino acid difference in the host APOBEC3G protein controls the primate species specificity of HIV type 1 virion infectivity factor. Proc. Natl. Acad. Sci. USA 101, 3770–3774 (2004).

    Article  CAS  Google Scholar 

  45. Mangeat, B., Turelli, P., Liao, S. & Trono, D. A single amino acid determinant governs the species-specific sensitivity of APOBEC3G to Vif action. J. Biol. Chem. 279, 14481–14483 (2004).

    Article  CAS  Google Scholar 

  46. Schröfelbauer, B., Chen, D. & Landau, N.R. A single amino acid of APOBEC3G controls its species-specific interaction with virion infectivity factor (Vif). Proc. Natl. Acad. Sci. USA 101, 3927–3932 (2004).

    Article  Google Scholar 

  47. Xu, H. et al. A single amino acid substitution in human APOBEC3G antiretroviral enzyme confers resistance to HIV-1 virion infectivity factor-induced depletion. Proc. Natl. Acad. Sci. USA 101, 5652–5657 (2004).

    Article  CAS  Google Scholar 

  48. Yamashita, T., Kamada, K., Hatcho, K., Adachi, A. & Nomaguchi, M. Identification of amino acid residues in HIV-1 Vif critical for binding and exclusion of APOBEC3G/F. Microbes Infect. 10, 1142–1149 (2008).

    Article  CAS  Google Scholar 

  49. Lavens, D. et al. Definition of the interacting interfaces of Apobec3G and HIV-1 Vif using MAPPIT mutagenesis analysis. Nucleic Acids Res. 38, 1902–1912 (2010).

    Article  CAS  Google Scholar 

  50. Shandilya, S.M., Bohn, M.F. & Schiffer, C.A. A computational analysis of the structural determinants of APOBEC3's catalytic activity and vulnerability to HIV-1 Vif. Virology 471–473, 105–116 (2014).

    Article  Google Scholar 

  51. Carlow, D.C., Short, S.A. & Wolfenden, R. Role of glutamate-104 in generating a transition state analogue inhibitor at the active site of cytidine deaminase. Biochemistry 35, 948–954 (1996).

    Article  CAS  Google Scholar 

  52. Chen, K.M. et al. Extensive mutagenesis experiments corroborate a structural model for the DNA deaminase domain of APOBEC3G. FEBS Lett. 581, 4761–4766 (2007).

    Article  CAS  Google Scholar 

  53. Bach, D. et al. Characterization of APOBEC3G binding to 7SL RNA. Retrovirology 5, 54 (2008).

    Article  Google Scholar 

  54. Bogerd, H.P. & Cullen, B.R. Single-stranded RNA facilitates nucleocapsid: APOBEC3G complex formation. RNA 14, 1228–1236 (2008).

    Article  CAS  Google Scholar 

  55. Wang, T. et al. 7SL RNA mediates virion packaging of the antiviral cytidine deaminase APOBEC3G. J. Virol. 81, 13112–13124 (2007).

    Article  CAS  Google Scholar 

  56. Zhang, L. et al. Function analysis of sequences in human APOBEC3G involved in Vif-mediated degradation. Virology 370, 113–121 (2008).

    Article  CAS  Google Scholar 

  57. Reingewertz, T.H. et al. Mapping the Vif-A3G interaction using peptide arrays: a basis for anti-HIV lead peptides. Bioorg. Med. Chem. 21, 3523–3532 (2013).

    Article  CAS  Google Scholar 

  58. Huthoff, H. & Malim, M.H. Identification of amino acid residues in APOBEC3G required for regulation by human immunodeficiency virus type 1 Vif and Virion encapsidation. J. Virol. 81, 3807–3815 (2007).

    Article  CAS  Google Scholar 

  59. Albin, J.S. et al. A single amino acid in human APOBEC3F alters susceptibility to HIV-1 Vif. J. Biol. Chem. 285, 40785–40792 (2010).

    Article  CAS  Google Scholar 

  60. Thompson, J.D., Higgins, D.G. & Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994).

    Article  CAS  Google Scholar 

  61. Hayashi, K. & Kojima, C. pCold-GST vector: a novel cold-shock vector containing GST tag for soluble protein production. Protein Expr. Purif. 62, 120–127 (2008).

    Article  Google Scholar 

  62. Ikura, M., Kay, L.E. & Bax, A. A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry 29, 4659–4667 (1990).

    Article  CAS  Google Scholar 

  63. Salzmann, M., Pervushin, K., Wider, G., Senn, H. & Wuthrich, K. TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc. Natl. Acad. Sci. USA 95, 13585–13590 (1998).

    Article  CAS  Google Scholar 

  64. Yamazaki, T., Lee, W., Arrowsmith, C.H., Muhandiram, D.R. & Kay, L.E. A suite of triple resonance NMR experiments for the backbone assignment of 15N, 13C, 2H labeled proteins with high sensitivity. J. Am. Chem. Soc. 116, 11655–11666 (1994).

    Article  CAS  Google Scholar 

  65. Jaipuria, G., Krishnarjuna, B., Mondal, S., Dubey, A. & Atreya, H.S. Amino acid selective labeling and unlabeling for protein resonance assignments. Adv. Exp. Med. Biol. 992, 95–118 (2012).

    Article  CAS  Google Scholar 

  66. Wuthrich, K. NMR of Proteins and Nucleic Acids (Wiley, New York, 1986).

  67. Wishart, D.S. et al. 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J. Biomol. NMR 6, 135–140 (1995).

    Article  CAS  Google Scholar 

  68. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).

    Article  CAS  Google Scholar 

  69. Schwieters, C.D., Kuszewski, J.J., Tjandra, N. & Clore, G.M. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160, 65–73 (2003).

    Article  CAS  Google Scholar 

  70. Cornilescu, G., Delaglio, F. & Bax, A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289–302 (1999).

    Article  CAS  Google Scholar 

  71. Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–55 (1996).

    Article  CAS  Google Scholar 

  72. Laskowski, R.A., Rullmannn, J.A., MacArthur, M.W., Kaptein, R. & Thornton, J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477–486 (1996).

    Article  CAS  Google Scholar 

  73. Albin, J.S., Hache, G., Hultquist, J.F., Brown, W.L. & Harris, R.S. Long-term restriction by APOBEC3F selects human immunodeficiency virus type 1 variants with restored Vif function. J. Virol. 84, 10209–10219 (2010).

    Article  CAS  Google Scholar 

  74. Haché, G., Shindo, K., Albin, J.S. & Harris, R.S. Evolution of HIV-1 isolates that use a novel Vif-independent mechanism to resist restriction by human APOBEC3G. Curr. Biol. 18, 819–824 (2008).

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by grants from the US National Institutes of Health (AI073167 to H.M. and GM091743 to R.S.H.). Salary support for T.K. was provided in part by a Toyobo Biotechnology Foundation Fellowship. The University of Minnesota Supercomputing and NMR center (US National Science Foundation, BIR-961477) provided NMR instrumentation. We thank C. Kojima (Institute for Protein Research, Osaka University) for the pCold vector, K. Strebel (US National Institutes of Health) for the pcDNA-hVif plasmid, M. Katahira for advice on structure calculations, Y. Iwatani for advice on degradation assays, Y. Xia for advice on NMR experiments, Y. Hong for supporting preparation of expression vectors, F. Liu for advice on human-cell experiments and K. Walters for editing the manuscript.

Author information

Authors and Affiliations

Authors

Contributions

T.K. designed the strategy for searching for soluble A3G NTD mutants and all A3G NTD mutants; performed harvest assays, Vif binding assays in E. coli, Vif-dependent degradation assays and deamination assays; prepared NMR samples; and determined the solution structure. E.M.L. performed single-cycle infectivity assays. M.S. optimized human-cell experiments. S.M.D.S. analyzed surface-charge distribution and binding-pocket volumes of the NTD structure. J.Z. provided support in harvest assays. L.C. and M.H. provided support with preparation of expression plasmids and with the Vif binding assay in E. coli. T.K., E.M.L., S.M.D.S., C.A.S., R.S.H. and H.M. contributed to writing and editing the manuscript.

Corresponding author

Correspondence to Hiroshi Matsuo.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Amino acid substitutions for increasing solubility of the A3G N-terminal domain.

(a) Amino acid sequence alignments of A3G NTD (NP_068594), sNTD (this study), consensus (this study), A3G CTD (NP_068594), A3B CTD (NP_004891) and A3A (NP_663745). Identical and mismatched amino acid residues between wild-type NTD and sNTD are shown in red and gray, respectively. Residue numbers correspond to wild-type A3G NTD. (b) Schematic presentation of amino acid sequences of sNTD and its variants. Residues identical to wild-type NTD are illustrated in red, whereas those that differ are indicated in gray. Black triangles indicate the location of residues that were substituted back to their endogenous amino acid identity with sNTD as a template. (c) Results of protein harvest assays showing solubility of sNTD variants. The band intensities of GST fused sNTD (lane 1), wild-type A3G NTD (lane 2), A3G CTD-2K3A (lane 3), and sNTD variants, including #1 - #12 of figure 1b, in a Coomassie gel were analyzed and normalized using the value of sNTD. The mean values ± s. d. for n = 3 independent cell cultures is plotted.

Supplementary Figure 2 Cα region of 1H, 13C HSQC spectra acquired on sNTD samples with selective 1H- and 13C-labeling by amino acid type.

Spectrum acquired on sNTD that was (a) uniformly 13C-labeled, (b) [1H, 13C]Ala-labeled, (c) [1H, 13C]Phe-labeled, (d) [1H, 13C]Ile-labeled, (e) [1H, 13C]Lys-labeled, (f) [1H, 13C]Leu-labeled, (g) [1H, 13C]Met-labeled, (h) [1H, 13C]Arg-labeled, (i) [1H, 13C]Thr-labeled, (j) [1H, 13C]Tyr-labeled, and (k) [1H, 13C]Val-labeled. Assignments are provided in spectra.

Supplementary Figure 3 1H-15N TROSY spectrum of sNTD.

Assignments of backbone amide protons are presented next to signals. Signals labeled with asterisks seem to arise from minor conformations. The inlet figure shows that major and minor signals for E38, V39 and K40.

Supplementary Figure 4 β-sheet conformation found in sNTD.

Inter-strand NOE connectivities are shown by double-headed arrows, and hydrogen bonds identified using an H/D-exchange experiment are indicated with red oval rectangles.

Supplementary Figure 5 Deamination and Vif binding assays.

(a-f) Deamination assays. 10mer DNA fragment, d(5’-ATTCCCAATT-3’), was used as a substrate for the deamination reaction. (a-c) display spectra of the substrate (a), the first deamination product d(5’-ATTCCUAATT-3’) (b) and the second deamination product d(5’-ATTCUUAATT-3’) (c). (d-e) Spectra of the substrate incubated with A3G CTD-2K3A for 30 minutes (d) and 24 hours (e). (f) Spectrum of the substrate after incubation with sNTD for 24 hours. (g) Representative SDS-PAGE gel images of the E. coli co-expression and GST-pull down assays used to identify residues critical for sNTD binding to Vif. Substituted residues are indicated on top of each gel image. In each gel, P, S and B show the amount of protein in pellet, soluble fraction and GST resin, respectively. The position of each protein is shown on the right side of the figure.

Supplementary Figure 6 Structural features of the zinc-coordinating region of sNTD.

(a) Stereoview of the zinc coordinating region of sNTD. α2 and α3 helices are colored green, the zinc ion is colored purple, and side chain atoms of zinc-coordinating residues, including H65, C97 and C100, and E67, are shown in ball-and-stick representation. Side chain atoms of L35, W90, I92 and M104 are located close to the zinc ion (see main text). (b) Comparison of the substrate-binding pocket and surface properties of sNTD, the A3G-NTD homology model (A3G NTD), and A3G-CTD. Top panels: Substrate-binding pocket volumes are presented as orange blobs, with the protein molecular surface shown as dark-blue mesh. Bottom panels: Molecular surface electrostatic potential are shown in red and blue for negative and positive charges, respectively. (bottom). Orientation of molecule is shown on left by cartoon models (Zn2+ is shown in purple). Location of D128 residue is shown in NTD structures. (c-d) A hydrophobic core formed by β1-α2-β3-α3. (c) Amino acid sequence alignment of wild-type A3G NTD, sNTD and A3 domains with available structures. Residue numbers refer to A3G NTD. Residues involved in the hydrophobic core are colored red. (d) A stereoview of the hydrophobic core in the sNTD structure.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 765 kb)

Supplementary Data Set 1

Uncropped gel images (PDF 2079 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kouno, T., Luengas, E., Shigematsu, M. et al. Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G. Nat Struct Mol Biol 22, 485–491 (2015). https://doi.org/10.1038/nsmb.3033

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.3033

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing