Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.72 kDa 
• Atom Count: 779 
• Modelled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique nucleic acid chains: 1

1N8X

Solution structure of HIV-1 Stem Loop SL1

• PDB DOI: 10.2210/pdb1N8X/pdb
• NDB: 1N8X
• BMRB: 5773

• Classification: RNA
• Mutation(s): No 


• Deposited: 2002-11-21 Released: 2003-04-08 
• Deposition Author(s): Lawrence, D.C., Stover, C.C., Noznitsky, J., Wu, Z., Summers, M.F.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 600 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Structure of the Intact Stem and Bulge of HIV-1 Psi-RNA Stem-Loop SL1

Lawrence, D.C., Stover, C.C., Noznitsky, J., Wu, Z., Summers, M.F.

(2003) J Mol Biol 326: 529-542

• PubMed: 12559920 
• DOI: 10.1016/s0022-2836(02)01305-0
• Primary Citation of Related Structures:  
  1N8X


• PubMed Abstract: 
  

The Psi-RNA packaging signal of the human immunodeficiency virus type-1 (HIV-1) genome contains a 35 nucleotide stem-loop, termed SL1, which is important for efficient genome packaging during virus assembly and for reverse transcription during infectivity. The predicted secondary structure of SL1 consists of an upper stem with a GC-rich loop that facilitates dimerization, a lower stem, and an intervening bulge (G5, A24-G25-G26) that is both strictly conserved and essential for efficient packaging of the viral genome. The structure of the upper stem in both the kissing and duplex dimer forms have been determined recently. Here, we report the structure of an engineered form of SL1 (SL1(m)) that contains a GAGA tetraloop substituted for the GC-rich loop. This construct does not aggregate and remains monomeric at concentrations up to 1mM, enabling structural studies of the intact stems and bulge. The structure was refined using 1H-13C residual dipolar couplings. The upper stem (C6-G12, C17-G23) is in close agreement with X-ray structures of kissing and duplex dimer forms of related oligoribonucleotides, and nucleotides C1-G4 and C27-G30 form the expected A-helical lower stem. Residues G5 and A24 of the predicted bulge form a G-A mismatch that stacks with the upper stem, and residues G25 and G26 stack between the G-A mismatch and the lower stem in a manner that produces a hole in the center of the bulge and a 25(+/-4) degrees bend between the upper and lower stems. SL1(m) exhibits relatively poor affinity for the HIV-1 nucleocapsid protein, suggesting that the bulge plays other roles in genome packaging.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250-5398, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
HIV-1 STEM LOOP SL1 MONOMERIC RNA	A	36	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 600 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 1N8X Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-21 
• Released Date: 2003-04-08 
Deposition Author(s): Lawrence, D.C., Stover, C.C., Noznitsky, J., Wu, Z., Summers, M.F.

Revision History  

• Version 1.0: 2003-04-08
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations