6XH0

Co-crystal structure of HIV-1 TAR RNA in complex with lab-evolved RRM TBP6.9

Summary for 6XH0

• Entry DOI: 10.2210/pdb6xh0/pdb
• Descriptor: TAR binding protein 6.9, TRANS-ACTIVATION RESPONSE ELEMENT, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: protein-rna complex, tar rna, lab-evolved protein, arginine fork, beta hairpin, major-groove readout, base triple, u1a, hiv-1, trans- activation, rna recognition motif, rrm, rna binding protein-rna complex, rna binding protein, rna binding protein/rna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 18777.47

Authors

Chavali, S.S.,Jenkins, J.L.,Wedekind, J.E. (deposition date: 2020-06-18, release date: 2020-10-14, Last modification date: 2024-03-06)

Primary citation

Chavali, S.S.,Mali, S.M.,Jenkins, J.L.,Fasan, R.,Wedekind, J.E.
Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.
J.Biol.Chem., 295:16470-16486, 2020

PubMed Abstract: RNA-protein interfaces control key replication events during the HIV-1 life cycle. The viral -activator of transcription (Tat) protein uses an archetypal arginine-rich motif (ARM) to recruit the host positive transcription elongation factor b (pTEFb) complex onto the viral -activation response (TAR) RNA, leading to activation of HIV transcription. Efforts to block this interaction have stimulated production of biologics designed to disrupt this essential RNA-protein interface. Here, we present four co-crystal structures of lab-evolved TAR-binding proteins (TBPs) in complex with HIV-1 TAR. Our results reveal that high-affinity binding requires a distinct sequence and spacing of arginines within a specific β2-β3 hairpin loop that arose during selection. Although loops with as many as five arginines were analyzed, only three arginines could bind simultaneously with major-groove guanines. Amino acids that promote backbone interactions within the β2-β3 loop were also observed to be important for high-affinity interactions. Based on structural and affinity analyses, we designed two cyclic peptide mimics of the TAR-binding β2-β3 loop sequences present in two high-affinity TBPs ( values of 4.2 ± 0.3 and 3.0 ± 0.3 nm). Our efforts yielded low-molecular weight compounds that bind TAR with low micromolar affinity ( values ranging from 3.6 to 22 μm). Significantly, one cyclic compound within this series blocked binding of the Tat-ARM peptide to TAR in solution assays, whereas its linear counterpart did not. Overall, this work provides insight into protein-mediated TAR recognition and lays the ground for the development of cyclic peptide inhibitors of a vital HIV-1 RNA-protein interaction.

PubMed: 33051202
DOI: 10.1074/jbc.RA120.015444

Experimental method

X-RAY DIFFRACTION (3.1 Å)