1EGK

CRYSTAL STRUCTURE OF A NUCLEIC ACID FOUR-WAY JUNCTION

• PDB DOI: https://doi.org/10.2210/pdb1EGK/pdb
• NAKB: 1EGK

• Classification: DNA-RNA HYBRID
• Mutation(s): No 


• Deposited: 2000-02-15 Released: 2000-06-26 
• Deposition Author(s): Nowakowski, J., Shim, P.J., Stout, C.D., Joyce, G.F.

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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) 

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

• PubMed: 10864501 
• 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.

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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.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.15 kDa 
• Atom Count: 2,338 
• Modelled Residue Count: 108 
• Deposited Residue Count: 108 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
10-23 DNA ENZYME	B, D	34	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	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 = 62.81	α = 90
b = 114.26	β = 90
c = 171.45	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-06-26 
Deposition Author(s): Nowakowski, J., Shim, P.J., Stout, C.D., Joyce, G.F.

Revision History  

• 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