1ZBN

Solution structure of BIV TAR hairpin complexed to JDV Tat arginine-rich motif


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A single intermolecular contact mediates intramolecular stabilization of both RNA and protein.

Calabro, V.Daugherty, M.D.Frankel, A.D.

(2005) Proc.Natl.Acad.Sci.Usa 102: 6849-6854

  • DOI: 10.1073/pnas.0409282102

  • PubMed Abstract: 
  • An arginine-rich peptide from the Jembrana disease virus (JDV) Tat protein is a structural "chameleon" that binds bovine immunodeficiency virus (BIV) or HIV TAR RNAs in two different binding modes, with an affinity for BIV TAR even higher than the co ...

    An arginine-rich peptide from the Jembrana disease virus (JDV) Tat protein is a structural "chameleon" that binds bovine immunodeficiency virus (BIV) or HIV TAR RNAs in two different binding modes, with an affinity for BIV TAR even higher than the cognate BIV peptide. We determined the NMR structure of the JDV Tat-BIV TAR high-affinity complex and found that the C-terminal tyrosine in JDV Tat forms a network of inter- and intramolecular hydrogen bonding and stacking interactions that simultaneously stabilize the beta-hairpin conformation of the peptide and a base triple in the RNA. A neighboring histidine also appears to help stabilize the peptide conformation. Induced fit binding is recurrent in protein-protein and protein-nucleic acid interactions, and the JDV Tat complex demonstrates how high affinity can be achieved not only by optimization of the binding interface but also by inducing new intramolecular contacts that stabilize each binding partner. Comparison to the cognate BIV Tat peptide-TAR complex shows how such a costabilization mechanism can evolve with only small changes to the peptide sequence. In addition, the bound structure of BIV TAR in the chameleon peptide complex is strikingly similar to the bound conformation of HIV TAR, suggesting new strategies for the development of HIV TAR binding molecules.


    Related Citations: 
    • An RNA-binding chameleon
      Smith, C.A.,Calabro, V.,Frankel, A.D.
      (2000) Mol.Cell 6: 1067
    • Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex
      Puglisi, J.D.,Chen, L.,Blanchard, S.,Frankel, A.D.
      (1995) Science 270: 1200


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143-2280, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
JDV tat protein
B
17Jembrana disease virusGene Names: tat
Find proteins for Q82854 (Jembrana disease virus)
Go to UniProtKB:  Q82854
Entity ID: 1
MoleculeChainsLengthOrganism
BIV mRNAA28N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 1ZBN Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance