1FIX | pdb_00001fix

THE STRUCTURE OF AN RNA/DNA HYBRID: A SUBSTRATE OF THE RIBONUCLEASE ACTIVITY OF HIV-1 REVERSE TRANSCRIPTASE

PDB DOI: https://doi.org/10.2210/pdb1FIX/pdb
NAKB: 1FIX

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

Deposited: 1996-10-24 Released: 1996-12-11
Deposition Author(s): Horton, N.C., Finzel, B.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Work:
0.145 (Depositor), 0.161 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The structure of an RNA/DNA hybrid: a substrate of the ribonuclease activity of HIV-1 reverse transcriptase.

Horton, N.C., Finzel, B.C.

(1996) J Mol Biology 264: 521-533

PubMed: 8969302 Search on PubMed
DOI: https://doi.org/10.1006/jmbi.1996.0658
Primary Citation Related Structures:
1FIX

PubMed Abstract:
The structure of a complementary hybrid duplex of RNA and DNA has been determined by X-ray crystallography. A ten residue DNA oligonucleotide of sequence 5'-G-G-C-G-C-C-C-G-A-A-3' was annealed to complementary RNA (5'-u-u-c-g-g-g-c-g-c-c-3') and crystallized, producing tetragonal crystals that diffract to 2.3 A resolution. The hybrid adopts a geometry that is neither strictly A nor B-form, rather the helix possesses qualities of both, reminiscent of spectroscopic descriptions of a hybrid conformation, or H-form. All of the ribonucleotides maintain the C3'-endo conformation seen in A-form, while both C3'-endo and C2'-endo conformations are found in the deoxyribonucleotides. The minor groove width (8.5 to 10.5 A) is intermediate between standard values for A (11 A) and B-form (7.4 A) DNA. The global parameters rise and base-pairs tilt (or inclination) are like that of A-DNA, however the slide and x displacement (Dx) are more like that of A-RNA, thus giving the hybrid a unique conformation. In addition, the 10-mer crystallizes in a manner that allows the formation of dimers that stack end-to-end, thereby providing a glimpse of how an extended (20 base-pair) helix of RNA-DNA hybrid might appear. This duplex sequence was selected for study because it is specifically recognized by the ribonuclease H function of HIV reverse transcriptase. A structure of a substrate of this enzyme is of potential value in understanding requirements for the selectivity of this important drug target. The minor groove of the hybrid duplex, lined with the 2-OH of the ribose rings, is the single distinguishing characteristic of the RNA/DNA hybrid, undoubtedly an important structural feature conferring selectivity.

Organizational Affiliation