437D | pdb_0000437d

CRYSTAL STRUCTURE OF AN RNA PSEUDOKNOT FROM BEET WESTERN YELLOW VIRUS INVOLVED IN RIBOSOMAL FRAMESHIFTING

• PDB DOI: https://doi.org/10.2210/pdb437D/pdb
• NAKB: 437D

• Classification: RNA
• Mutation(s): No 


• Deposited: 1998-11-24 Released: 1998-12-03 
• Deposition Author(s): Su, L., Chen, L., Egli, M., Berger, J.M., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot.

Su, L., Chen, L., Egli, M., Berger, J.M., Rich, A.

(1999) Nat Struct Biol 6: 285-292

• PubMed: 10074948 
• DOI: https://doi.org/10.1038/6722
• Primary Citation Related Structures: 
  437D


• PubMed Abstract: 
  

  Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. A pseudoknot has two stems that form a quasi-continuous helix and two connecting loops. A 1.6 A crystal structure of the beet western yellow virus (BWYV) pseudoknot reveals rotation and a bend at the junction of the two stems. A loop base is inserted in the major groove of one stem with quadruple-base interactions. The second loop forms a new minor-groove triplex motif with the other stem, involving 2'-OH and triple-base interactions, as well as sodium ion coordination. Overall, the number of hydrogen bonds stabilizing the tertiary interactions exceeds the number involved in Watson-Crick base pairs. This structure will aid mechanistic analyses of ribosomal frameshifting.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.29 kDa 
• Atom Count: 766 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.08	α = 90
b = 30.08	β = 90
c = 140.08	γ = 120

Software Package:

Software Name	Purpose
MIRAS	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-12-03 
Deposition Author(s): Su, L., Chen, L., Egli, M., Berger, J.M., Rich, A.

Revision History  

• Version 1.0: 1998-12-03
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Derived calculations