1BVJ

HIV-1 RNA A-RICH HAIRPIN LOOP

• PDB DOI: https://doi.org/10.2210/pdb1BVJ/pdb
• NAKB: 1BVJ

• Classification: RNA
• Organism(s): Human immunodeficiency virus type 1 (MAL ISOLATE)
• Mutation(s): No 


• Deposited: 1998-08-31 Released: 1998-12-09 
• Deposition Author(s): Puglisi, E.V., Puglisi, J.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 160 
• Conformers Submitted: 21 
• Selection Criteria: LOWEST TOTAL AND RESTRAINT VIOLATION ENERGIES 

Literature

HIV-1 A-rich RNA loop mimics the tRNA anticodon structure.

Puglisi, E.V., Puglisi, J.D.

(1998) Nat Struct Biol 5: 1033-1036

• PubMed: 9846871 
• DOI: https://doi.org/10.1038/4141
• Primary Citation of Related Structures:  
  1BVJ


• PubMed Abstract: 
  

  Interaction of HIV-1 genomic RNA and human tRNA(Lys)3 initiates viral reverse transcription. An adenosine-rich (A-rich) loop in HIV RNA mediates complex formation between tRNA and viral RNA. We have determined the structure of an A-rich loop oligonucleotide using nuclear magnetic resonance spectroscopy. The loop structure is stabilized by a noncanonical G-A pair and a U-turn motif, which leads to stacking of the conserved adenosines. The structure has similarity to the tRNA anticodon structure, and suggests possible mechanisms for its role in initiation of reverse transcription.

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Organizational Affiliation: 

Department of Structural Biology, Stanford University School of Medicine, California 94305-5400, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.4 kDa 
• Atom Count: 493 
• Modelled Residue Count: 23 
• Deposited Residue Count: 23 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*GP*CP*GP*AP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*AP*UP*CP*UP*CP*GP*CP* C)-3')	A	23	Human immunodeficiency virus type 1 (MAL ISOLATE)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 160 
• Conformers Submitted: 21 
• Selection Criteria: LOWEST TOTAL AND RESTRAINT VIOLATION ENERGIES 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-12-09 
Deposition Author(s): Puglisi, E.V., Puglisi, J.D.

Revision History  

• Version 1.0: 1998-12-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Database references, Derived calculations