Macromolecule Content

• Total Structure Weight: 9827.97 
• Atom Count: 649 
• Residue Count: 30 
• Unique nucleic acid chains: 1

1AJU

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

• DOI: 10.2210/pdb1AJU/pdb
• NDB: 1AJU

• Classification: RNA


• Deposited: 1997-05-10 Released: 1997-12-17 
• Deposition Author(s): Brodsky, A.S., Williamson, J.R.

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Experimental Data Snapshot

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

Literature

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

Brodsky, A.S., Williamson, J.R.

(1997) J.Mol.Biol. 267: 624-639

• PubMed: 9126842 
• 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 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.

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Related Citations: 

• 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
• 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
• 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
• 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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
TAR RNA	A	30	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ARG	A	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

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

Software Package:

Software Name	Purpose
X-PLOR	refinement
X-PLOR	phasing
X-PLOR	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-05-10 
• Released Date: 1997-12-17 
• Deposition Author(s): Brodsky, A.S., Williamson, J.R.

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