Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

• Published in: eLife 2016-10, Vol.5
• Main Authors: Schulze-Gahmen, Ursula, Echeverria, Ignacia, Stjepanovic, Goran, Bai, Yun, Lu, Huasong, Schneidman-Duhovny, Dina, Doudna, Jennifer A, Zhou, Qiang, Sali, Andrej, Hurley, James H
• Format: Article
• Language: English
• Subjects: Arginine; BASIC BIOLOGICAL SCIENCES; Biochemistry; Biophysics and Structural Biology; Crystal structure; Cyclin T - chemistry; Cyclin T - metabolism; Cyclin-Dependent Kinase 9 - chemistry; Cyclin-Dependent Kinase 9 - metabolism; Deuterium Exchange Measurement; DNA, Viral - chemistry; DNA, Viral - metabolism; HDX; HIV; HIV Long Terminal Repeat; HIV-1 - genetics; Human immunodeficiency virus; Humans; Hydrogen-deuterium exchange; integrative modeling; Life Sciences & Biomedicine - Other Topics; Magnetic Resonance Spectroscopy; Medical research; Models, Molecular; Proteins; Proviruses - genetics; Repressor Proteins - chemistry; Repressor Proteins - metabolism; Ribonucleic acid; RNA; SAXS; Scattering, Small Angle; SHAPE; Solvents; tat Gene Products, Human Immunodeficiency Virus - chemistry; tat Gene Products, Human Immunodeficiency Virus - metabolism; Tat protein; Transcription; Transcription, Genetic; Transcriptional Elongation Factors - chemistry; Transcriptional Elongation Factors - metabolism; X-ray crystallography; Zinc
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.15910

HIV-1 Tat hijacks the human superelongation complex (SEC) to promote proviral transcription. Here we report the 5.9 Å structure of HIV-1 TAR in complex with HIV-1 Tat and human AFF4, CDK9, and CycT1. The TAR central loop contacts the CycT1 Tat-TAR recognition motif (TRM) and the second Tat Zn -binding loop. Hydrogen-deuterium exchange (HDX) shows that AFF4 helix 2 is stabilized in the TAR complex despite not touching the RNA, explaining how it enhances TAR binding to the SEC 50-fold. RNA SHAPE and SAXS data were used to help model the extended (Tat Arginine-Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop. The structure and functional assays collectively support an integrative structure and a bipartite binding model, wherein the TAR central loop engages the CycT1 TRM and compact core of Tat, while the TAR major groove interacts with the extended Tat ARM.