1G4Q

RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG

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

  • Deposited: 2000-10-27 Released: 2003-07-08 
  • Deposition Author(s): Han, G.W.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.143 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution.

Han, G.W.

(2001) Acta Crystallogr D Biol Crystallogr 57: 213-218

  • DOI: 10.1107/s0907444900017595
  • Primary Citation of Related Structures:  
    1G4Q

  • PubMed Abstract: 
  • For the first time, ab initio direct methods have been used to solve the crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence corresponds to the leftmost two-thirds of the polypurine tract (PPT), the primer for second-strand DNA synthesis by HIV-1 reverse transcriptase (RT) ...

    For the first time, ab initio direct methods have been used to solve the crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence corresponds to the leftmost two-thirds of the polypurine tract (PPT), the primer for second-strand DNA synthesis by HIV-1 reverse transcriptase (RT). Direct methods using Shake-and-Bake (SnB) yielded solutions for the RNA/DNA decamer molecule using 1.15 A data, which is just on the resolution edge of what might work with direct methods. Atomic positions for 96% of the entire molecule, containing 514 non-H atoms including three Ca(2+) ions, were easily interpreted from a Fourier map based on the 'Shake-and-Bake' minimal function and CROQUE phase-refinement program. Only six atoms, primarily in the sugar linkage, were missing in this Fourier map. At present, the R factor of the model is 0.143 (R(free) = 0.186) for the 562 non-H atom sites located. The conformation of the RNA/DNA helix is A-form, with a typical A-helix minor-groove width. This paper presents the methodology used in solving this structure.


    Related Citations: 
    • An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H.
      Kopka, M.L., Lavelle, L., Han, G.W., Ng, H.L., Dickerson, R.E.
      (2003) J Mol Biol 334: 653

    Organizational Affiliation

    Molecular Biology Institute, University of California at Los Angles, Los Angeles, CA 90095-1570, USA. gyewon@mbi.ucla.edu



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'A10N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'B10N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MPD
      Query on MPD

      Download Ideal Coordinates CCD File 
      F [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
      C6 H14 O2
      SVTBMSDMJJWYQN-YFKPBYRVSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      C [auth A], D [auth A], E [auth A]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.15 Å
      • R-Value Free: 0.186 
      • R-Value Work: 0.143 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 25.699α = 90
      b = 41.067β = 90
      c = 46.113γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SHELXL-97refinement

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      • Deposited Date: 2000-10-27 
      • Released Date: 2003-07-08 
      • Deposition Author(s): Han, G.W.

      Revision History  (Full details and data files)

      • Version 1.0: 2003-07-08
        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