Legends for Supporting Information files

Figure S1. Superposition of HIV-1 IN CCD.

A superposition of the IN CCD using eight HIV-1 IN structures (PDB codes: 1B9F (6), 1BI4 (7), 1BIS (5), 1BL3 (7), 1EX4 (2), 1QS4 (4), 2B4J (3), and 2ITG (1)) was prepared using PyMOL software (version 0.97). The catalytic triad residues (D64, D116, and E152) are shown in green. Amino acid residues conferring resistance to EVG as primary mutations (T66, E92, F121, Q146, and S147) and secondary mutations (H51, Q95, E138, and E157) are shown in red and cyan, respectively. Regions encompassing residues 47-56 (yellow) and 140-152 (pink) demonstrate multiple conformations.

Figure S2. Protein sequence alignment of INs.

Amino acid sequences of HIV-1BH10 (GenBank accession number: M15654), HIV-2EHO (U27200), HIV-2ROD (M15390), SIVmac239 (M33262), bovine immunodeficiency virus (BIV) (NC_001413), human T cell leukemia virus type I (HTLV-I) (J02029), Moloney MLV (MoMLV) (J02255), and feline leukemia virus (FeLV) (M18247) were aligned using the program Clustal W (8) and the region corresponding to the CCD of HIV-1BH10 (residues 50-212) is represented. Absolutely conserved residues and conservative substitutions are shown in black and gray boxes, respectively. Symbols above sequences: closed circle, primary mutation for EVG resistance; open circle, secondary mutation for EVG resistance; asterisk, catalytic triad residues (D64, D116, and E152); dashed line, flexible loop (residues 140-152).

References

1. Bujacz, G., J. Alexandratos, Z. L. Qing, C. Clement-Mella, and A. Wlodawer. 1996. The catalytic domain of human immunodeficiency virus integrase: ordered active site in the F185H mutant. FEBS Lett 398:175-8.

2. Chen, J. C., J. Krucinski, L. J. Miercke, J. S. Finer-Moore, A. H. Tang, A. D. Leavitt, and 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 97:8233-8.

3. Cherepanov, P., A. L. Ambrosio, S. Rahman, T. Ellenberger, and A. Engelman. 2005. Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. Proc Natl Acad Sci U S A 102:17308-13.

4. Goldgur, Y., R. Craigie, G. H. Cohen, T. Fujiwara, T. Yoshinaga, T. Fujishita, H. Sugimoto, T. Endo, H. Murai, and D. R. Davies. 1999. Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design. Proc Natl Acad Sci U S A 96:13040-3.

5. Goldgur, Y., F. Dyda, A. B. Hickman, T. M. Jenkins, R. Craigie, and D. R. Davies. 1998. Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium. Proc Natl Acad Sci U S A 95:9150-4.

6. Greenwald, J., V. Le, S. L. Butler, F. D. Bushman, and S. Choe. 1999. The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity. Biochemistry 38:8892-8.

7. Maignan, S., J. P. Guilloteau, Q. Zhou-Liu, C. Clement-Mella, and V. Mikol. 1998. Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. J Mol Biol 282:359-68.

8. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-80.

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