Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.58 kDa 
• Atom Count: 775 
• Modelled Residue Count: 47 
• Deposited Residue Count: 47 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2KX5

Recognition of HIV TAR RNA by peptide mimetic of Tat protein

• PDB DOI: 10.2210/pdb2KX5/pdb
• NDB: 2KX5
• BMRB: 16941

• Classification: RNA binding protein/RNA
• Mutation(s): No 


• Deposited: 2010-04-26 Released: 2010-07-07 
• Deposition Author(s): Davidson, A., Patora-Komisarska, K., Robinson, J., Varani, G.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations and lowest energy 

Literature

Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein.

Davidson, A., Patora-Komisarska, K., Robinson, J.A., Varani, G.

(2011) Nucleic Acids Res 39: 248-256

• PubMed: 20724442 
• DOI: 10.1093/nar/gkq713
• Primary Citation of Related Structures:  
  2KX5


• PubMed Abstract: 
  

The pharmacological disruption of the interaction between the HIV Tat protein and its cognate transactivation response RNA (TAR) would generate novel anti-viral drugs with a low susceptibility to drug resistance, but efforts to discover ligands with sufficient potency to warrant pharmaceutical development have been unsuccessful. We have previously described a family of structurally constrained β-hairpin peptides that potently inhibits viral growth in HIV-infected cells. The nuclear magnetic resonance (NMR) structure of an inhibitory complex revealed that the peptide makes intimate contacts with the 3-nt bulge and the upper helix of the RNA hairpin, but that a single residue contacts the apical loop where recruitment of the essential cellular co-factor cyclin T₁ occurs. Attempting to extend the peptide to form more interactions with the RNA loop, we examined a library of longer peptides and achieved > 6-fold improvement in affinity. The structure of TAR bound to one of the extended peptides reveals that the peptide slides down the major groove of the RNA, relative to our design, in order to maintain critical interactions with TAR. These conserved contacts involve three amino acid side chains and identify critical interaction points required for potent and specific binding to TAR RNA. They constitute a template of essential interactions required for inhibition of this RNA.

---

Organizational Affiliation: 

Department of Chemistry, University of Washington, Seattle, WA 98195, USA,

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic peptide mimetic of Tat protein	B	18	N/A	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
HIV TAR RNA	A	29	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations and lowest energy 
• OLDERADO: 2KX5 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-26 
• Released Date: 2010-07-07 
Deposition Author(s): Davidson, A., Patora-Komisarska, K., Robinson, J., Varani, G.

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance