1EGK

CRYSTAL STRUCTURE OF A NUCLEIC ACID FOUR-WAY JUNCTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Alternative conformations of a nucleic acid four-way junction.

Nowakowski, J.Shim, P.J.Stout, C.D.Joyce, G.F.

(2000) J Mol Biol 300: 93-102

  • DOI: 10.1006/jmbi.2000.3826
  • Primary Citation of Related Structures:  
    1EGK

  • PubMed Abstract: 
  • A crystal structure of a 108 nucleotide RNA-DNA complex containing a four-way junction was solved at 3.1 A resolution. The structure of the junction differs substantially from the "stacked-X" conformation observed previously, due to a 135 degrees rotation of the branches ...

    A crystal structure of a 108 nucleotide RNA-DNA complex containing a four-way junction was solved at 3.1 A resolution. The structure of the junction differs substantially from the "stacked-X" conformation observed previously, due to a 135 degrees rotation of the branches. Comparison of the two conformers provides insight into the factors contributing to the flexibility of four-way junctions. The stacked-X conformation maximizes base-stacking but causes unfavorable repulsion between phosphate groups, whereas the 135 degrees -rotated "crossed" conformation minimizes electrostatic clashes at the expense of reduced base-stacking. Despite the large rotation of the branches, both junction structures exhibit an antiparallel arrangement of the continuous strands and opposite polarity of the crossover strands.


    Organizational Affiliation

    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*GP*GP*AP*GP*AP*GP*AP*GP*AP*UP*GP*GP*GP*UP*GP*CP*GP*AP*G)-3')A, C20N/A
    Protein Feature View
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    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 2
    MoleculeChainsLengthOrganismImage
    10-23 DNA ENZYMEB, D34N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.10 Å
    • R-Value Free: 0.258 
    • R-Value Work: 0.226 
    • R-Value Observed: 0.230 
    • Space Group: I 2 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 62.81α = 90
    b = 114.26β = 90
    c = 171.45γ = 90
    Software Package:
    Software NamePurpose
    SOLVEphasing
    X-PLORrefinement
    MOSFLMdata reduction
    CCP4data scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2000-06-26
      Type: Initial release
    • Version 1.1: 2008-04-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2018-01-31
      Changes: Experimental preparation