1RRR

RNA DUPLEX CONTAINING A PURINE-RICH STRAND, NMR, 10 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 32 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST POTENTIAL ENERGY AND MINIMAL VIOLATIONS AND ACCEPTABLE STEREOCHEMISTRY 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes.

Gyi, J.I.Lane, A.N.Conn, G.L.Brown, T.

(1998) Biochemistry 37: 73

  • DOI: 10.1021/bi9719713
  • Primary Citation of Related Structures:  
    1AXP, 1DRR, 1RRD, 1RRR

  • PubMed Abstract: 
  • The structures of d(GAAGAGAAGC).d(GCTTCTCTTC), d(GAAGAGAAGC). r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), and r(GAAGAGAAGC). r(GCUUCUCUUC) have been determined in solution from NMR data. Globally, the pure DNA and RNA duplexes were in the B and A forms, respectively ...

    The structures of d(GAAGAGAAGC).d(GCTTCTCTTC), d(GAAGAGAAGC). r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), and r(GAAGAGAAGC). r(GCUUCUCUUC) have been determined in solution from NMR data. Globally, the pure DNA and RNA duplexes were in the B and A forms, respectively. The two DNA.RNA hybrids were neither A nor B, but closer globally to the A than the B form. However, the thermodynamically less stable d(GAAGAGAAGC).r(GCUUCUCUUC) duplex has a significantly different conformation from r(GAAGAGAAGC). d(GCTTCTCTTC). Structures were calculated based on the NMR data, using restrained molecular dynamics. A new approach to the treatment of conformational averaging based on a prioriprobabilities has been used. The nucleotides were treated by fitting the scalar coupling data and NOE time courses to a two-state model comprising N and S sugar puckers each with a different glycosidic torsion angle, and the mole fraction of the S state. Restraint sets for different distributions of N and S states within molecules were constructed, such that each nucleotide was weighted in the ensemble according to the mole fractions (or a prioriprobabilities). The individual nucleotide conformations were strongly restrained, whereas the internucleotide restraints were set relatively loosely. Ensembles of conformations were generated and assessed by comparison of the NOEs calculated from ensemble-averaged relaxation matrices with the experimental NOEs. The ensemble averages accounted for the experimental data much better than any individual member, or for structures calculated assuming a single unique conformation. The two hybrids populated different degrees of conformational space. There was a general trend in minor and major groove widths in the order d(GAAGAGAAGC).d(GCTTCTCTTC), d(GAAGAGAAGC).r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), r(GAAGAGAAGC).r(GCUUCUCUUC) and a similar progression in global character from B-like to A-like structures. Furthermore, r(GAAGAGAAGC).d(GCTTCTCTTC) showed a greater dispersion of conformations in the ensemble than d(GAAGAGAAGC).r(GCUUCUCUUC), reflecting the greater flexibility of the sugars. If conformational averaging of the nucleotides is ignored, incorrect virtual structures are produced that nevertheless are able to satisfy a substantial fraction of the experimental data.


    Related Citations: 
    • Comparison of the Thermodynamic Stabilities and Solution Conformations of DNA.RNA Hybrids Containing Purine-Rich and Pyrimidine-Rich Strands with DNA and RNA Duplexes
      Gyi, J.I., Conn, G.L., Lane, A.N., Brown, T.
      (1996) Biochemistry 35: 12538

    Organizational Affiliation

    Division of Molecular Structure, National Institute of Medical Research, London, UK.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3')A 10N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*CP*UP*UP*CP*UP*CP*UP*UP*C)-3')B 10N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 32 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST POTENTIAL ENERGY AND MINIMAL VIOLATIONS AND ACCEPTABLE STEREOCHEMISTRY 
  • OLDERADO: 1RRR Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations, Other