2RPK

Solution Structure of Domain II of the Positive Polarity CCHMVD Hammerhead Ribozyme


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 
  • Selection Criteria: minimized average structure of 33 converged conformers with the least restraint violation energy and total energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1093/nar/gkn918
  • Primary Citation of 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.


  • Organizational Affiliation

    Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46012 Valencia, Spain.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3')20N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 60 
  • Conformers Submitted: 
  • Selection Criteria: minimized average structure of 33 converged conformers with the least restraint violation energy and total energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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