ArticleNucleic acids research2014
Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 68 citations in OpenAlex.
- Molecular Docking of Natural Products: Critical Appraisal of Current Methodology and Practical Guidelines.Molecules (Basel, Switzerland) · 2026Review
- Structural Basis of Polypurine Track Strand Displacement by HIV-1 Reverse Transcriptase.bioRxiv : the preprint server for biology · 2026Article
- Endogenous Retroviruses in Host-Virus Coevolution: From Genomic Domestication to Functional Innovation.Genes · 2025Review
- Structural basis for the evolution of a domesticated group II intron-like reverse transcriptase to function in host cell DNA repair.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structural basis of deoxynucleotide addition by HIV-1 RT during reverse transcription.Nature communications · 2024Article
- Internal RNA 2'-O-methylation on the HIV-1 genome impairs reverse transcription.Nucleic acids research · 2024Article
- Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- Biophysical Characterization of p51 and p66 Monomers of HIV-1 Reverse Transcriptase with Their Inhibitors.The protein journal · 2023Article
- Mechanism of protein-primed template-independent DNA synthesis by Abi polymerases.Nucleic acids research · 2022Article
- Cryo-EM structures of Escherichia coli Ec86 retron complexes reveal architecture and defence mechanism.Nature microbiology · 2022Article
- Insights into HIV-1 Reverse Transcriptase (RT) Inhibition and Drug Resistance from Thirty Years of Structural Studies.Viruses · 2022Review
- Flexibility of telomerase in binding the RNA template and DNA telomeric repeat.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Structures of Substrate Complexes of Foamy Viral Protease-Reverse Transcriptase.Journal of virology · 2021Article
- Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex.Nature communications · 2021Article
- Retroviral RNase H: Structure, mechanism, and inhibition.The Enzymes · 2021Review
- Advances in understanding the initiation of HIV-1 reverse transcription.Current opinion in structural biology · 2020Review
- Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches.Biochemistry · 2020Article
- Cutting into the Substrate Dominance: Pharmacophore and Structure-Based Approaches toward Inhibiting Human Immunodeficiency Virus Reverse Transcriptase-Associated Ribonuclease H.Accounts of chemical research · 2020Review
- Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer.Current research in structural biology · 2020Article
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4 authors at 1 institution in 1 country.
Funding
Abstract
In synthesizing a double-stranded DNA from viral RNA, HIV-1 reverse transcriptase (RT) generates an RNA/DNA intermediate. RT also degrades the RNA strand and synthesizes the second DNA strand. The RNase H active site of RT functions as a nuclease to cleave the RNA strand; however, the structural basis for endonucleolytic cleavage of the RNA strand remains elusive. Here we report crystal structures of RT-RNA/DNA-dATP and RT-RNA/DNA-nevirapine (NVP) ternary complexes at 2.5 and 2.9 Å resolution, respectively. The polymerase region of RT-RNA/DNA-dATP complex resembles DNA/DNA ternary complexes apart from additional interactions of 2'-OH groups of the RNA strand. The conformation and binding of RNA/DNA deviates significantly after the seventh nucleotide versus a DNA/DNA substrate. Binding of NVP slides the RNA/DNA non-uniformly over RT, and the RNA strand moves closer to the RNase H active site. Two additional structures, one containing a gapped RNA and another a bulged RNA, reveal that conformational changes of an RNA/DNA and increased interactions with the RNase H domain, including the interaction of a 2'-OH with N474, help to position the RNA nearer to the active site. The structures and existing biochemical data suggest a nucleic acid conformation-induced mechanism for guiding cleavage of the RNA strand.
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