title: Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.
abstract: 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 Zn2+-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.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.|California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.
authors.forename: Ursula
authors.initials: U
authors.lastname: Schulze-Gahmen
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.|Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.|California Institute of Quantitative Biosciences, University of California San, Francisco, San Francisco, United States.
authors.forename: Ignacia
authors.identifier: 0000-0003-4717-1467
authors.initials: I
authors.lastname: Echeverria
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.|California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.|Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.
authors.forename: Goran
authors.identifier: 0000-0002-4841-9949
authors.initials: G
authors.lastname: Stjepanovic
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.|California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.
authors.forename: Yun
authors.initials: Y
authors.lastname: Bai
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.|California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.
authors.forename: Huasong
authors.initials: H
authors.lastname: Lu
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.|Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.|California Institute of Quantitative Biosciences, University of California San, Francisco, San Francisco, United States.
authors.forename: Dina
authors.initials: D
authors.lastname: Schneidman-Duhovny
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.|California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.|Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.|Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.|Department of Chemistry, University of California, Berkeley, Berkeley, United States.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Doudna
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.|California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhou
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.|Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.|California Institute of Quantitative Biosciences, University of California San, Francisco, San Francisco, United States.
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.|California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.|Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.
authors.forename: James H
authors.identifier: 0000-0001-5054-5445
authors.initials: JH
authors.lastname: Hurley
mesh_terms: D056906:Cyclin T / Q000737:chemistry* / Q000378:metabolism; D042863:Cyclin-Dependent Kinase 9 / Q000737:chemistry* / Q000378:metabolism; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism; D041961:Deuterium Exchange Measurement; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D011533:Proviruses / Q000235:genetics; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism; D053838:Scattering, Small Angle; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000737:chemistry* / Q000378:metabolism; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000737:chemistry* / Q000378:metabolism
chemical_list: C471348:AFF4 protein, human; C503684:CCNT1 protein, human; D056906:Cyclin T; D004279:DNA, Viral; D012097:Repressor Proteins; D035602:Transcriptional Elongation Factors; D054322:tat Gene Products, Human Immunodeficiency Virus; C467969:CDK9 protein, human; D042863:Cyclin-Dependent Kinase 9
keywords: HDX; SAXS; SHAPE; X-ray crystallography; biochemistry; biophysics; integrative modeling; structural biology; virus