4PWD

Crystal structure of HIV-1 reverse transcriptase in complex with bulge-RNA/DNA and Nevirapine

Summary for 4PWD

• Entry DOI: 10.2210/pdb4pwd/pdb
• Related: 1HYS 3V4D 3V4I 3V81 4PQU 4PUO 4Q0B
• Descriptor: HIV-1 Reverse Transcriptase, P66 subunit, HIV-1 Reverse Transcriptase, P51 subunit, 5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*U)-3', ... (7 entities in total)
• Functional Keywords: fingers, palm, thumb, connection, rnase h, nucleotidyltransferase, dna-directed dna polymerase, rna-directed dna polymerase, nuclease, ribonuclease h, trna, transferase, hydrolase-dna-rna-inhibitor complex, hydrolase/dna/rna/inhibitor
• Biological source: Human immunodeficiency virus type 1 (HIV-1); More
• Cellular location: Matrix protein p17: Virion (Potential). Capsid protein p24: Virion (Potential). Nucleocapsid protein p7: Virion (Potential). Reverse transcriptase/ribonuclease H: Virion (Potential). Integrase: Virion (Potential): P03366 P03366
• Total number of polymer chains: 8
• Total formula weight: 259151.40

Authors

Das, K.,Martinez, S.E.,Arnold, E. (deposition date: 2014-03-19, release date: 2014-06-18, Last modification date: 2023-09-20)

Primary citation

Das, K.,Martinez, S.E.,Bandwar, R.P.,Arnold, E.
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.
Nucleic Acids Res., 42:8125-8137, 2014

PubMed 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.

PubMed: 24880687
DOI: 10.1093/nar/gku487

Experimental method

X-RAY DIFFRACTION (3 Å)