Biological Assembly 1  

 3D View: Structure | Electron Density

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.25 kDa 
• Atom Count: 691 
• Residue Count: 28 
• Unique nucleic acid chains: 1

1L3D

Low Resolution Crystal Structure of a Viral RNA Pseudoknot

• DOI: 10.2210/pdb1L3D/pdb
• NDB: UR0021

• Classification: RNA
• Mutation(s): No 


• Deposited: 2002-02-26 Released: 2002-03-22 
• Deposition Author(s): Egli, M., Minasov, G., Su, L., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.275 
• R-Value Work: 0.271 

Literature

Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution.

Egli, M., Minasov, G., Su, L., Rich, A.

(2002) Proc Natl Acad Sci U S A 99: 4302-4307

• PubMed: 11904368 
• DOI: 10.1073/pnas.062055599
• Primary Citation of Related Structures:  
  1L2X, 1L3D


• PubMed Abstract: 
  

Many pathogenic viruses use programmed -1 ribosomal frameshifting to regulate translation of their structural and enzymatic proteins from polycistronic mRNAs. Frameshifting is commonly stimulated by a pseudoknot located downstream from a slippery sequence, the latter positioned at the ribosomal A and P sites. We report here the structures of two crystal forms of the frameshifting RNA pseudoknot from beet western yellow virus at resolutions of 1.25 and 2.85 A. Because of the very high resolution of 1.25 A, ten mono- and divalent metal ions per asymmetric unit could be identified, giving insight into potential roles of metal ions in stabilizing the pseudoknot. A magnesium ion located at the junction of the two pseudoknot stems appears to play a crucial role in stabilizing the structure. Because the two crystal forms exhibit mostly unrelated packing interactions and local crystallographic disorder in the high-resolution form was resolvable, the two structures offer the most detailed view yet of the conformational preference and flexibility of an RNA pseudoknot.

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Organizational Affiliation: 

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA pseudoknot	A	28	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.275 
• R-Value Work: 0.271 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.81	α = 90
b = 107.81	β = 90
c = 107.81	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-02-26 
• Released Date: 2002-03-22 
Deposition Author(s): Egli, M., Minasov, G., Su, L., Rich, A.

Revision History 

• Version 1.0: 2002-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance