1EGK

CRYSTAL STRUCTURE OF A NUCLEIC ACID FOUR-WAY JUNCTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.226 

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

  • 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 rot ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
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
Entity ID: 2
MoleculeChainsLengthOrganism
10-23 DNA ENZYMEB,D34N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.226 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 62.810α = 90.00
b = 114.260β = 90.00
c = 171.450γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SOLVEphasing
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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