2RO2 | pdb_00002ro2

Solution structure of domain I of the negative polarity CChMVd hammerhead ribozyme

• PDB DOI: https://doi.org/10.2210/pdb2RO2/pdb
• NAKB: 2RO2

• Classification: RNA
• Mutation(s): No 


• Deposited: 2008-03-05 Released: 2008-12-30 
• Deposition Author(s): Gallego, J., Dufour, D., Gago, S., de la Pena, M., Flores, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: Structures with the least restraint violations and total energy 

Literature

Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads

Dufour, D., de la Pena, M., Gago, S., Flores, R., Gallego, J.

(2009) Nucleic Acids Res 37: 368-381

• PubMed: 19043070 
• DOI: https://doi.org/10.1093/nar/gkn918
• Primary Citation Related Structures: 
  2RO2, 2RPK


• PubMed Abstract: 
  

  Loop-loop tertiary interactions play a key role in the folding and catalytic activity of natural hammerhead ribozymes. Using a combination of NMR spectroscopy, site-directed mutagenesis and kinetic and infectivity analyses, we have examined the structure and function of loops 1 and 2 of the (+) and (-) hammerheads of chrysanthemum chlorotic mottle viroid RNA. In both hammerheads, loop 1 is a heptanucleotide hairpin loop containing an exposed U at its 5' side and an extrahelical U at its 3'-side critical for the catalytic activity of the ribozyme in vitro and for viroid infectivity in vivo, whereas loop 2 has a key opened A at its 3'-side. These structural features promote a specific loop-loop interaction motif across the major groove. The essential features of this tertiary structure element, base pairing between the 5' U of loop 1 and the 3' A of loop 2, and interaction of the extrahelical pyrimidine of loop 1 with loop 2, are likely shared by a significant fraction of natural hammerheads.

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Organizational Affiliation: 
• Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46012 Valencia, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.44 kDa 
• Atom Count: 492 
• Modeled Residue Count: 23 
• Deposited Residue Count: 23 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3')	A	23	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: Structures with the least restraint violations and total energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-30 
Deposition Author(s): Gallego, J., Dufour, D., Gago, S., de la Pena, M., Flores, R.

Revision History  

• Version 1.0: 2008-12-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-05-29
  Changes: Data collection