6XH3

Co-crystal structure of HIV-1 TAR RNA in complex with lab-evolved RRM TBP6.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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This is version 1.1 of the entry. See complete history


Literature

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.

Chavali, S.S.Mali, S.M.Jenkins, J.L.Fasan, R.Wedekind, J.E.

(2020) J Biol Chem 

  • DOI: 10.1074/jbc.RA120.015444
  • Primary Citation of Related Structures:  
    6XH1, 6XH0, 6XH3, 6XH2

  • PubMed Abstract: 
  • RNA-protein interfaces control key replication events during the HIV-1 lifecycle. The viral trans -activator of transcription (Tat) protein uses an archetypal ARM (arginine-rich motif) to recruit the host positive transcription elongation fac ...

    RNA-protein interfaces control key replication events during the HIV-1 lifecycle. The viral trans -activator of transcription (Tat) protein uses an archetypal ARM (arginine-rich motif) to recruit the host positive transcription elongation factor b (pTEFb) complex onto the viral trans -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 ( K D values of 4.2 ± 0.3 nM and 3.0 ± 0.3 nM). Our efforts yielded low molecular weight compounds that bind TAR with low micromolar affinity ( K D values ranging from 3.6-22 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.


    Organizational Affiliation

    Department of Biochemistry & Biophysics, University of Rochester, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TAR BINDING PROTEIN TBP 6.3A88Homo sapiensMutation(s): 0 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
NIH Common Fund Data Resources
PHAROS  P09012
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
TRANS-ACTIVATION RESPONSE ELEMENTD27Human immunodeficiency virus 1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.602α = 90
b = 40.602β = 90
c = 291.98γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAI150463

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references