1EGK | pdb_00001egk

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 (Depositor) 
  • R-Value Work: 
    0.226 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 Biology 300: 93-102

  • DOI: https://doi.org/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. 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   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
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, C
20N/A
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
10-23 DNA ENZYME
B, D
34N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.258 (Depositor) 
  • R-Value Work:  0.226 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
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

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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
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations