1N4L

A DNA analogue of the polypurine tract of HIV-1

Summary for 1N4L

• Entry DOI: 10.2210/pdb1n4l/pdb
• Related: 1D1U 1DOE 1I6J 1N85 1QAI 1QAJ
• Descriptor: 5'-D(*CP*TP*TP*TP*TP*TP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3', 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*G)-3', Reverse Transcriptase, ... (4 entities in total)
• Functional Keywords: mmlv rt; polypurine tract; hiv-1; asymmetric dna; protein-dna complex, transferase-dna complex, transferase/dna
• Biological source: Moloney murine leukemia virus
• Cellular location: Gag-Pol polyprotein: Host cell membrane ; Lipid-anchor . Matrix protein p15: Virion . Capsid protein p30: Virion . Nucleocapsid protein p10: Virion : P03355
• Total number of polymer chains: 3
• Total formula weight: 38725.73

Authors

Cote, M.L.,Pflomm, M.,Georgiadis, M.M. (deposition date: 2002-10-31, release date: 2003-06-24, Last modification date: 2024-10-02)

Primary citation

Cote, M.L.,Pflomm, M.,Georgiadis, M.M.
Staying Straight with A-tracts: A DNA Analog of the HIV-1 Polypurine Tract
J.Mol.Biol., 330:57-74, 2003

PubMed Abstract: The polypurine tract (PPT) from the HIV-1 genome is resistant to digestion by reverse transcriptase following (-)-strand synthesis and is used to prime (+)-strand synthesis during retroviral replication. We have determined the crystal structure of the asymmetric DNA/DNA analog16-mer duplex (CTTTTTAAAAGAAAAG/CTTTTCTTTTAAAAAG) comprising most of the "visible" portion of the RNA:DNA hybrid from the polypurine tract of HIV-1, which was previously reported in a complex with HIV-1 reverse transcriptase. Our 16-mer completely encompasses a 10-mer DNA duplex analog of the HIV-1 PPT. We report here a detailed analysis of our B' form 16-mer DNA structure, including three full pure A-tracts, as well as a comparative structural analysis with polypurine tract and other A-tract-containing nucleic acid structures. Our analysis reveals that the polypurine tract structures share structural features despite being different nucleic acid forms (i.e. DNA:DNA versus RNA:DNA). In addition, the previously reported A-tract-containing DNA molecules bound to topoisomerase I are remarkably similar to our polypurine tract 16-mer structure. On the basis of our analysis, we suggest that the specific topology of long pure A-tracts is remarkably comparable across a wide array of biological environments.

PubMed: 12818202
DOI: 10.1016/S0022-2836(03)00554-0

Experimental method

X-RAY DIFFRACTION (2 Å)