1JB8 | pdb_00001jb8

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

• PDB DOI: https://doi.org/10.2210/pdb1JB8/pdb
• NAKB: 1JB8

• Classification: DNA/RNA
• Mutation(s): No 


• Deposited: 2001-06-02 Released: 2003-07-01 
• Deposition Author(s): Han, G.W., Kopka, M.L., Langs, D., Dickerson, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.251 (Depositor) 
• R-Value Work: 
  0.223 (Depositor), 0.238 (DCC) 

Starting Model: experimental

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 U S A 100: 9214-9219

• PubMed: 12872000 
• DOI: https://doi.org/10.1073/pnas.1533326100
• Primary Citation Related Structures: 
  1JB8


• 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 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.

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Organizational Affiliation: 
• Molecular Biology Institute, University of California, Los Angeles, CA 90095-1570, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.25 kDa 
• Atom Count: 480 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'	A	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'	B	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.251 (Depositor) 
• R-Value Work:  0.223 (Depositor), 0.238 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.234	α = 90
b = 46.78	β = 90
c = 56.56	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
EPMR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-01 
Deposition Author(s): Han, G.W., Kopka, M.L., Langs, D., Dickerson, R.E.

Revision History  

• Version 1.0: 2003-07-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references
• Version 1.5: 2024-04-03
  Changes: Refinement description