246D

STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C) , WITH A 3'-TERMINAL DEOXY RESIDUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the purine-pyrimidine alternating RNA double helix, r(GUAUAUA)d(C), with a 3'-terminal deoxy residue.

Wahl, M.C.Ban, C.Sekharudu, C.Ramakrishnan, B.Sundaralingam, M.

(1996) Acta Crystallogr D Biol Crystallogr 52: 655-667

  • DOI: 10.1107/S0907444996000248
  • Primary Citation of Related Structures:  
    246D

  • PubMed Abstract: 
  • The crystal structure of the purine-pyrimidine alternating octameric RNA helix, r(GUAUAUA)d(C), carrying a 3'-terminal deoxycytidine residue, has been determined at 2.2 A resolution. The molecule crystallizes in the rhombohedral space group R3 (hexagonal cell constants: a = b = 43 ...

    The crystal structure of the purine-pyrimidine alternating octameric RNA helix, r(GUAUAUA)d(C), carrying a 3'-terminal deoxycytidine residue, has been determined at 2.2 A resolution. The molecule crystallizes in the rhombohedral space group R3 (hexagonal cell constants: a = b = 43.07,c = 59.36 A;alpha = beta = 90,gamma = 120 degrees )with one duplex in an asymmetric unit. The structure was solved by molecular replacement and refined with 83 and 2/3 solvent molecules and 2/3 sodium ions to a final R factor of 15.6% using 1775 reflections (86%). The duplexes are approximately linear, their global helix axes are inclined by 10 degrees with respect to the 3(2)-screw axes, and they are stacked on top of each other in a head-to-tail fashion. The twist between the junction base pairs of the stacked duplexes is negligible resulting in a discontinuity of the helix backbones and grooves. The sodium ions on the threefold axis play a significant role in the organization of the packing network. The helical parameters, particularly the twist and the roll, of this alternating sequence are in accord with Calladine's rules. Almost all the 2'-hydroxyl groups are involved in specific hydrogen-bonding interactions, either directly to the sugar ring oxygens O4' on the 3' side, or, through water bridges, to the sugars, phosphates, or bases. This hydrogen bonding of the 2'-hydroxyl groups restrains the conformation of the sugar-phosphate backbone and the glycosidic torsion angles of this RNA fragment. The lack of intermolecular packing contacts in the grooves provides a clear picture of the groove solvation.


    Organizational Affiliation

    The Ohio State University, Laboratory of Biological Macromolecular Structure, Department of Biochemistry, Columbus 43210-1002, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA/RNA (5'-R(*GP*UP*AP*UP*AP*UP*AP*)-D(*C)-3')A, B8N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NA
    Query on NA

    Download Ideal Coordinates CCD File 
    C [auth B], D [auth B]SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Work: 0.156 
    • R-Value Observed: 0.156 
    • Space Group: H 3
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 43.1α = 90
    b = 43.1β = 90
    c = 59.4γ = 120
    Software Package:
    Software NamePurpose
    X-PLORrefinement
    XENGENdata reduction

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1996-08-26
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance