1D96

MOLECULAR STRUCTURE OF R(GCG)D(TATACGC): A DNA-RNA HYBRID HELIX JOINED TO DOUBLE HELICAL DNA

• PDB DOI: https://doi.org/10.2210/pdb1D96/pdb
• NAKB: 1D96

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


• Deposited: 1992-10-17 Released: 1993-07-15 
• Deposition Author(s): Wang, A.H.-J., Fujii, S., Van Boom, J.H., Van Der Marel, G.A., Van Boeckel, S.A.A., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.160 

Literature

Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA.

Wang, A.H., Fujii, S., van Boom, J.H., van der Marel, G.A., van Boeckel, S.A., Rich, A.

(1982) Nature 299: 601-604

• PubMed: 6181416 
• DOI: https://doi.org/10.1038/299601a0
• Primary Citation of Related Structures:  
  1D96


• PubMed Abstract: 
  

  The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA--RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.19 kDa 
• Atom Count: 410 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*GP*CP*GP*)-D(*TP*AP*TP*AP*CP*GP*C)-3')	A, B	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.2	α = 90
b = 43.46	β = 90
c = 49.4	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-07-15 
Deposition Author(s): Wang, A.H.-J., Fujii, S., Van Boom, J.H., Van Der Marel, G.A., Van Boeckel, S.A.A., Rich, A.

Revision History  

• Version 1.0: 1993-07-15
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references