Primary Citation PubMed: 22266819
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Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.
(2013) Nat Struct Mol Biol 20
PubMed: 23314251 | PubMedCentral: PMC3973182 | DOI: 10.1038/nsmb.2485
Structural comparison with the recently reported RT–DNA–NNRTI complex 29 (PDB: 3V81) turned out to be not as revealing.
( a ) Pairwise comparisons of RT in the 3V81 structure with RT complexed with Nevirapine (3QIP 14 ), an RT ternary complex (1RTD 26 ), and our WT22Efv (4B3O).
Perhaps due to the crosslinking between RT and DNA and the procedure of soaking NNRTI into a preformed RT–DNA co-crystal, the protein structure of 3V81 is more similar to that of the RT–DNA–dNTP ternary complex than to that in either the RT–NNRTI complex or our WT22Efv structure ( Fig. 3a ).
Publication Year: 2013
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.
(2014) Nucleic Acids Res 42
PubMed: 24880687 | PubMedCentral: PMC4081091 | DOI: 10.1093/nar/gku487
The minor groove widths of two independent copies of DNA/DNA in RT-DNA/DNA-NVP (yellow and orange; PDB ID 3V81) and RT-DNA/DNA-AZTTP (blue and cyan; PDB ID 3V4I) structures by CURVES+ are plotted.
Atomic coordinates of an RT molecule in RT-DNA/DNA-AZTTP (PDB ID 3V4I) or RT-DNA/DNA-NVP (PDB ID 3V81) complexes ( 37 ) were used as starting models to locate the two copies of RT in RT-RNA/DNA-dATP or RT-RNA/DNA-NVP complexes, respectively, by molecular replacement.
In contrast, the conformation of DNA/DNA (Figure 3D ) is less perturbed upon binding of NVP when previously reported structures of RT-DNA/DNA-NVP (PDB ID 3V81) and RT-DNA/DNA-AZTTP (PDB ID 3V4I) obtained in an analogous crystal form were compared ( 37 ).
Publication Year: 2014
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