1JB8

The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of an RNADNA hybrid reveals intermolecular intercalation: Dimer formation by base-pair swapping

Han, G.W.Kopka, M.L.Langs, D.Sawaya, M.R.Dickerson, R.E.

(2003) Proc.Natl.Acad.Sci.USA 100: 9214-9219

  • DOI: 10.1073/pnas.1533326100

  • PubMed Abstract: 
  • An intermolecular intercalation of base pairs was found at the CA step in the I222 crystal structure of the RNA.DNA hybrid, r(CAAAGAAAAG).d(CTTTTCTTTG), which contains two-thirds of the polypurine tract sequence of HIV-1 with a substitution of cytosi ...

    An intermolecular intercalation of base pairs was found at the CA step in the I222 crystal structure of the RNA.DNA hybrid, r(CAAAGAAAAG).d(CTTTTCTTTG), which contains two-thirds of the polypurine tract sequence of HIV-1 with a substitution of cytosine for the initial adenine. This sequence crystallized in both P212121 and I222 space groups, with an rms difference of only 0.63 A between residues 3 to 18 of the two forms. P212121 and I222 helices are both A-like, but intercalation occurs only in the I222 crystal form. The present structure shows bases stacked in parallel rather than perpendicular as in intercalated DNA (I-DNA). The base intercalation is also different from zipper-like meshing of bases seen in the center of the crystal structure of d(GCGAAAGCT), which does not have Watson-Crick base pairing. The base-step intercalation seen here is reminiscent of domain swapping in proteins; therefore, we call this phenomenon "base-pair swapping." It involves a highly mobile CA step and seems to be sequence-specific and electrostatically stable without disrupting Watson-Crick interactions. It also exhibits a large rise concurrent with unwinding of the helix (low twist). We present a base-pair swapping dimer in nucleic acids.


    Organizational Affiliation

    Molecular Biology Institute, University of California, Los Angeles, CA 90095-1570, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'A10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'B10N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.223 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 45.234α = 90.00
b = 46.780β = 90.00
c = 56.560γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description