1AJU

HIV-2 TAR-ARGININAMIDE COMPLEX, NMR, 20 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINTS AND LOWEST ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the HIV-2 TAR-argininamide complex.

Brodsky, A.S.Williamson, J.R.

(1997) J.Mol.Biol. 267: 624-639

  • DOI: 10.1006/jmbi.1996.0879
  • Primary Citation of Related Structures:  1AKX

  • PubMed Abstract: 
  • The trans-activating region (TAR) RNA-Tat protein interaction is important for activation of transciption in the human immunodeficiency virus (HIV). A model complex for this interaction composed of the two base bulge HIV-2 TAR and the amide derivativ ...

    The trans-activating region (TAR) RNA-Tat protein interaction is important for activation of transciption in the human immunodeficiency virus (HIV). A model complex for this interaction composed of the two base bulge HIV-2 TAR and the amide derivative of arginine was studied by multidimensional heteronuclear NMR. Because of the improved spectral properties of the HIV-2 TAR complex, a larger number of NOEs in the bulge region were observed than in earlier studies of the HIV-1 TAR-argininamide complex. A total of 681 NOE distance restraints were collected and used to determine the solution structure of the HIV-2 TAR-argininamide complex. As observed in the previously proposed model from this lab, the two A-form stems co-axially stack and the critical U23 and the argininamide are located in the major groove. Model calculations including non-experimental restraints indicate that U23 is within hydrogen bonding distance to A27 consistent with the formation of a U x A x U base-triple. Base-triple formation helps open the major groove to increase the accessibility of G26 to hydrogen bond donors from the guanidinium group of argininamide. Argininamide binding is stabilized by stacking of the guanidinium group between the bases of A22 and U23, forming an argininamide sandwich.


    Related Citations: 
    • 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
    • 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
    • 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
    • Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents
      Gelbin, A.,Schneider, B.,Clowny, L.,Hsieh, S.-H.,Olsen, W.K.,Berman, H.M.
      (1996) J.Am.Chem.Soc. 118: 519


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
TAR RNAA30N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG

Download SDF File 
Download CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINTS AND LOWEST ENERGY 
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance