1ARJ

ARG-BOUND TAR RNA, NMR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 20 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein.

Aboul-ela, F.Karn, J.Varani, G.

(1995) J.Mol.Biol. 253: 313-332

  • DOI: 10.1006/jmbi.1995.0555
  • Also Cited By: 1UUI, 1UUD

  • PubMed Abstract: 
  • The human immunodeficiency virus type-1 (HIV-1) Tat protein stimulates transcriptional elongation. Tat is introduced to the transcription machinery by binding to the transactivation response region (TAR) RNA stem-loop encoded by the 5' leader sequenc ...

    The human immunodeficiency virus type-1 (HIV-1) Tat protein stimulates transcriptional elongation. Tat is introduced to the transcription machinery by binding to the transactivation response region (TAR) RNA stem-loop encoded by the 5' leader sequence found on all HIV-1 mRNAs. We have used multidimensional heteronuclear NMR to determine the structure of the TAR RNA in the presence of the ADP-1 polypeptide, a 37-mer that carries the minimal RNA recognition region of the Tat protein and closely mimics Tat binding specificity. In the presence of a variety of ligands, including ADP-1, related basic peptides and the amino acid derivative argininamide, the bulge region of TAR undergoes a local conformational rearrangement and forms a more stable structure. The structure of TAR in the bound form has been determined from over 1000 NMR-derived constraints. The U23 residue at the 5' end of the bulge is positioned near G26 and A27 in the major groove, rather than stacked on A22 as in the free TAR. U23 and G26 are brought into close proximity by contacts to the guanidinium group and side-chain amide group of a common arginine residue. However, the interaction of this guanidinium group with TAR is not the only source of binding specificity. Besides NOEs to the arginine residue participating in the conformational change, ADP-1 shows additional intermolecular NOEs to TAR, suggesting that there are multiple points of contacts between TAR RNA and residues from the basic and core regions of Tat. These structural results provide important clues towards the identification of small molecular mass and/or peptidomimetic inhibitors of the essential Tat-TAR interaction.


    Related Citations: 
    • Role of RNA Structure in Arginine Recognition of Tar RNA
      Puglisi, J.D.,Chen, L.,Frankel, A.D.,Williamson, J.R.
      (1993) Proc.Natl.Acad.Sci.USA 90: 3680
    • Conformation of the Tar RNA-Arginine Complex by NMR Spectroscopy
      Puglisi, J.D.,Tan, R.,Calnan, B.J.,Frankel, A.D.,Williamson, J.R.
      (1992) Science 257: 76
    • Hydrogen-Bonding Contacts in the Major Groove are Required for Human Immunodeficiency Virus Type-1 Tat Protein Recognition of Tar RNA
      Hamy, F.,Asseline, U.,Grasby, J.,Iwai, S.,Pritchard, C.,Slim, G.,Butler, P.J.,Karn, J.,Gait, M.J.
      (1993) J.Mol.Biol. 230: 111
    • High Affinity Binding of Tar RNA by the Human Immunodeficiency Virus Type-1 Tat Protein Requires Base-Pairs in the RNA Stem and Amino Acid Residues Flanking the Basic Region
      Churcher, M.J.,Lamont, C.,Hamy, F.,Dingwall, C.,Green, S.M.,Lowe, A.D.,Butler, J.G.,Gait, M.J.,Karn, J.
      (1993) J.Mol.Biol. 230: 90


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
TAR RNAN29N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG

Download SDF File 
Download CCD File 
N
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ARGKd: 1000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 20 
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance