1BN0

SL3 HAIRPIN FROM THE PACKAGING SIGNAL OF HIV-1, NMR, 11 STRUCTURES

• PDB DOI: https://doi.org/10.2210/pdb1BN0/pdb
• BMRB: 4175
• NAKB: 1BN0

• Classification: RNA
• Mutation(s): No 


• Deposited: 1998-07-31 Released: 1999-04-27 
• Deposition Author(s): Pappalardo, L., Kerwood, D.J., Pelczer, I., Borer, P.N.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 11 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Literature

Three-dimensional folding of an RNA hairpin required for packaging HIV-1.

Pappalardo, L., Kerwood, D.J., Pelczer, I., Borer, P.N.

(1998) J Mol Biol 282: 801-818

• PubMed: 9743628 
• DOI: https://doi.org/10.1006/jmbi.1998.2046
• Primary Citation of Related Structures:  
  1BN0


• PubMed Abstract: 
  

  An NMR-based structure is presented for a 20 mer hairpin model of the SL3 stem-loop from the HIV-1 packaging signal. The stem has an A-family structure. However, the GGAG tetraloop appears to be flexible with the second (G10) and fourth (G12) bases extruded from the normal stacking arrangement. The A-base (A11) occupies a cavity large enough for it to jump rapidly between stacking upon G9 (in the loop) and G13 (from the base-pair adjacent to the loop). The H-bonding loci of G10, A11, and G12 are unoccupied in the free RNA structure. The loop should be easily adaptable to binding by the HIV-1 nucleocapsid protein or loop receptors.

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Organizational Affiliation: 

Department of Chemistry, Syracuse University, Syracuse, NY, 13244-4100, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.48 kDa 
• Atom Count: 429 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
SL3 RNA HAIRPIN	A	20	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 11 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-27 
Deposition Author(s): Pappalardo, L., Kerwood, D.J., Pelczer, I., Borer, P.N.

Revision History  

• Version 1.0: 1999-04-27
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-05-22
  Changes: Data collection