1AJL

FIVE-NUCLEOTIDE BULGE LOOP FROM TETRAHYMENA THERMOPHILA GROUP I INTRON


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution conformation of a five-nucleotide RNA bulge loop from a group I intron.

Luebke, K.J.Landry, S.M.Tinoco, I.

(1997) Biochemistry 36: 10246-10255

  • DOI: 10.1021/bi9701540
  • Primary Citation of Related Structures:  1AJT

  • PubMed Abstract: 
  • We present the solution conformation, determined by NMR spectroscopy, of a five-nucleotide RNA bulge loop. The bulge interrupts the stem of a 25-nucleotide RNA hairpin, and its sequence and flanking sequences are those of a conserved bulge from a Gro ...

    We present the solution conformation, determined by NMR spectroscopy, of a five-nucleotide RNA bulge loop. The bulge interrupts the stem of a 25-nucleotide RNA hairpin, and its sequence and flanking sequences are those of a conserved bulge from a Group I intron. The secondary structure of the bulge loop in the hairpin context is that predicted by the secondary structure prediction algorithm of Zuker. It differs, however, from the secondary structure deduced from sequence covariation of the bulge in the context of the functionally folded Group I introns and observed in the crystal structure of an independently folding domain of the Group I intron from Tetrahymena thermophila. This difference represents an exception to the heierarchical model of RNA folding in which preformed elements of secondary structure interact to form a tertiary structure. The three-dimensional structure of the bulge loop is characterized by discontinuous base stacking. Adjacent adenines stack with each other and with the flanking double helices. However, the position of the central uracil is not well defined by NOE distance constraints and is a point of discontinuity in the base stacking.


    Organizational Affiliation

    Department of Chemistry, University of California at Berkeley, Berkeley, California 94720-1460, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*UP*AP*AP*UP*AP*AP*GP*CP*UP*C)-3')A12Tetrahymena thermophila
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*AP*GP*UP*AP*CP*C)-3')B7Tetrahymena thermophila
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance