1G4Q

RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG

Summary for 1G4Q

• Entry DOI: 10.2210/pdb1g4q/pdb
• Descriptor: 5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3', 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3', CALCIUM ION, ... (5 entities in total)
• Functional Keywords: rna/dna hybrid, polypurine tract of hiv-1, direct methods, dna-rna complex, dna-rna hybrid
• Total number of polymer chains: 2
• Total formula weight: 6485.45

Authors

Han, G.W. (deposition date: 2000-10-27, release date: 2003-07-08, Last modification date: 2024-02-07)

Primary citation

Han, G.W.
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution.
Acta Crystallogr.,Sect.D, 57:213-218, 2001

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). 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.

PubMed: 11173466
DOI: 10.1107/S0907444900017595

Experimental method

X-RAY DIFFRACTION (1.15 Å)