Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.59 kDa 
• Atom Count: 567 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

2LQZ

Structure of the RNA claw of the DNA packaging motor of bacteriophage 29

• PDB DOI: 10.2210/pdb2LQZ/pdb
• NDB: 2LQZ
• BMRB: 18336

• Classification: RNA
• Mutation(s): No 


• Deposited: 2012-03-19 Released: 2012-08-01 
• Deposition Author(s): Harjes, E.J., Matsuo, H.J., Kitamura, A.J.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 9 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of the RNA claw of the DNA packaging motor of bacteriophage 29.

Harjes, E., Kitamura, A., Zhao, W., Morais, M.C., Jardine, P.J., Grimes, S., Matsuo, H.

(2012) Nucleic Acids Res 40: 9953-9963

• PubMed: 22879380 
• DOI: 10.1093/nar/gks724
• Primary Citation of Related Structures:  
  2LQZ


• PubMed Abstract: 
  

Bacteriophage DNA packaging motors translocate their genomic DNA into viral heads, compacting it to near-crystalline density. The Bacillus subtilis phage 29 has a unique ring of RNA (pRNA) that is an essential component of its motor, serving as a scaffold for the packaging ATPase. Previously, deletion of a three-base bulge (18-CCA-20) in the pRNA A-helix was shown to abolish packaging activity. Here, we solved the structure of this crucial bulge by nuclear magnetic resonance (NMR) using a 27mer RNA fragment containing the bulge (27b). The bulge actually involves five nucleotides (17-UCCA-20 and A100), as U17 and A100 are not base paired as predicted. Mutational analysis showed these newly identified bulge residues are important for DNA packaging. The bulge introduces a 33-35° bend in the helical axis, and inter-helical motion around this bend appears to be restricted. A model of the functional 120b pRNA was generated using a 27b NMR structure and the crystal structure of the 66b prohead-binding domain. Fitting this model into a cryo-EM map generated a pentameric pRNA structure; five helices projecting from the pRNA ring resemble an RNA claw. Biochemical analysis suggested that this shape is important for coordinated motor action required for DNA translocation.

---

Organizational Affiliation: 

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (27-MER)	A	27	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 9 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2LQZ Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-19 
• Released Date: 2012-08-01 
Deposition Author(s): Harjes, E.J., Matsuo, H.J., Kitamura, A.J.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2012-11-07
  Changes: Database references