Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.96 kDa 
• Atom Count: 726 
• Modelled Residue Count: 34 
• Deposited Residue Count: 34 
• Unique nucleic acid chains: 1

2D19

Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the kissing-loop dimer

• PDB DOI: 10.2210/pdb2D19/pdb
• NDB: 2D19

• Classification: RNA
• Mutation(s): No 


• Deposited: 2005-08-15 Released: 2005-11-01 
• Deposition Author(s): Baba, S., Takahashi, K., Noguchi, S., Takaku, H., Koyanagi, Y., Yamamoto, N., Kawai, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 11 
• Selection Criteria: structures with the lowest energy 

Literature

Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers.

Baba, S., Takahashi, K., Noguchi, S., Takaku, H., Koyanagi, Y., Yamamoto, N., Kawai, G.

(2005) J Biochem 138: 583-592

• PubMed: 16272570 
• DOI: 10.1093/jb/mvi158
• Primary Citation of Related Structures:  
  2D17, 2D18, 2D19, 2D1A, 2D1B


• PubMed Abstract: 
  

Dimer formation of HIV-1 genomic RNA through its dimerization initiation site (DIS) is crucial to maintaining infectivity. Two types of dimers, the initially generated kissing-loop dimer and the subsequent product of the extended-duplex dimer, are formed in the stem-bulge-stem region with a loop including a self-complementary sequence. NMR chemical shift analysis of a 39mer RNA corresponding to DIS, DIS39, in the kissing-loop and extended-duplex dimers revealed that the three dimensional structures of the stem-bulge-stem region are extremely similar between the two types of dimers. Therefore, we designed two shorter RNA molecules, loop25 and bulge34, corresponding to the loop-stem region and the stem-bulge-stem region of DIS39, respectively. Based upon the chemical shift analysis, the conformation of the loop region of loop25 is identical to that of DIS39 for each of the two types of dimers. The conformation of bulge34 was also found to be the same as that of the corresponding region of DIS39. Thus, we determined the solution structures of loop25 in each of the two types of dimers as well as that of bulge34. Finally, the solution structures of DIS39 in the kissing-loop and extended-duplex dimers were determined by combining the parts of the structures. The solution structures of the two types of dimers were similar to each other in general with a difference found only in the A16 residue. The elucidation of the structures of DIS39 is important to understanding the molecular mechanism of the conformational dynamics of viral RNA molecules.

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Organizational Affiliation: 

Department of Life and Environmental Sciences, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)-3'	A, B	17	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 11 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2D19 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-15 
• Released Date: 2005-11-01 
Deposition Author(s): Baba, S., Takahashi, K., Noguchi, S., Takaku, H., Koyanagi, Y., Yamamoto, N., Kawai, G.

Revision History  

• Version 1.0: 2005-11-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations