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Crystal structure of HIV-1 Tat complexed with human P-TEFb

Abstract

Regulation of the expression of the human immunodeficiency virus (HIV) genome is accomplished in large part by controlling transcription elongation. The viral protein Tat hijacks the host cell’s RNA polymerase II elongation control machinery through interaction with the positive transcription elongation factor, P-TEFb, and directs the factor to promote productive elongation of HIV mRNA. Here we describe the crystal structure of the Tat·P-TEFb complex containing HIV-1 Tat, human Cdk9 (also known as CDK9), and human cyclin T1 (also known as CCNT1). Tat adopts a structure complementary to the surface of P-TEFb and makes extensive contacts, mainly with the cyclin T1 subunit of P-TEFb, but also with the T-loop of the Cdk9 subunit. The structure provides a plausible explanation for the tolerance of Tat to sequence variations at certain sites. Importantly, Tat induces significant conformational changes in P-TEFb. This finding lays a foundation for the design of compounds that would specifically inhibit the Tat·P-TEFb complex and block HIV replication.

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Figure 1: Overall structure of the Tat·P-TEFb·ATP.
Figure 2: Structure of P-TEFb-bound Tat.
Figure 3: The Tat-interacting areas of P-TEFb.
Figure 4: Comparison of the crystal structures of P-TEFb·ATP and Tat·P-TEFb·ATP.
Figure 5: A conservation-dependent location of Tat’s amino acid residues.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for Tat·P-TEFb and Tat·P-TEFb·ATP structures have been deposited in the Protein Data Bank with accession numbers 3mi9 and 3mia, respectively.

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Acknowledgements

We thank J. Lovelace and G. E. Borgstahl for maintenance and management of the Eppley Institute’s X-ray Crystallography facility; D. G. Vassylyev for the zonal scaling instruction files. This work is supported by the NIH grants GM35500 and AI074392 to D.H.P., by Nebraska Department of Health and Human Services grant LB506 and in part by NIH grant GM082923 to T.H.T. This work is also based on research conducted at the Advanced Photon Source on the Northeastern Collaborative Access Team beamlines, which are supported by award RR-15301 from the National Center for Research Resources at the National Institutes of Health. Use of the Advanced Photon Source is supported by the US Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. The Eppley Institute’s X-ray Crystallography facility is supported by Cancer Center Support Grant P30CA036727.

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T.H.T. managed the crystallization and structure determination part of the project, solved the crystal structures and prepared the manuscript. N.D.B. obtained the crystals. Diffraction data collection was performed by N.D.B. and T.H.T. Protein cloning, expression, purification and writing the corresponding methods sections were performed by S.C.S., K.V. and J.J.C., respectively. D.H.P. managed the protein production part of the project, and helped generate and edit the manuscript.

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Correspondence to Tahir H. Tahirov.

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Tahirov, T., Babayeva, N., Varzavand, K. et al. Crystal structure of HIV-1 Tat complexed with human P-TEFb. Nature 465, 747–751 (2010). https://doi.org/10.1038/nature09131

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