Primary Citation PubMed: 11080630
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The mutation T477A in HIV-1 reverse transcriptase (RT) restores normal proteolytic processing of RT in virus with Gag-Pol mutated in the p51-RNH cleavage site.
(2010) Retrovirology 7
PubMed: 20122159 | PubMedCentral: PMC2831009 | DOI: 10.1186/1742-4690-7-6
Specifically, the superposition of the RNH domains of several RT structures shows notable variability in the main chain conformation; and in some cases (e.g., PDB 1FK9 [ 31 ]), parts of the β-... heet (residues 444 - 454) are missing, possibly due to poor electron density resulting from multiple conformations in this region.
Publication Year: 2010
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
Two distinct RT conformations in nucleic-acid complexes In our RT–hybrid complexes, the protein is more similar to previously reported structures of apo-RT with an NNRTI (PDB: 1FK9, 3QIP) 14 ,... 20 , 22 than RT–nucleic acid complexes ( Fig. 2a–c , Supplementary Fig. 4 ), thus removing the distinction between “open” apo and “closed” nucleic acid-bound conformations.
Structures were solved by molecular replacement using the RT from the ternary complex (1RTD) and RT with NNRTI (1FK9) 22 , 26 with MolRep in CCP4 56 .
Publication Year: 2013
Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors.
(2012) Biology (Basel) 1
PubMed: 24832224 | PubMedCentral: PMC4009785 | DOI: 10.3390/biology1020222
Two separate clusters of structures are apparent in this data, where we have labelled the two groups A and B. All structures in group A (including 1FK9,1IKW and 1VRT) show p51 flexibility in their sec... nd ANM modes, whereas those in group B do not.
Figure 4 The fluctuations of the NNRTI bound HIV-1 RT described by the second ANM mode for ( a ) the EFV bound 1FK9 and ( b ) NVP bound 1RTH structures.
In ( c ) the 1IKW (EFV) and 1VRT (NVP) bound structures are compared, more of the low modes show high levels of similarity than in the plot for 1FK9 and 1RTH shown in Figure 2 c. Figure 7 Comparison of the squared fluctuations predicted by ANM mode 2 of the NVP bound 1VRT (red) and EFV bound 1IKW structures (black).
Figure 3 Comparison of the first 15 ANM modes generated from the apo HIV-1 RT structure and those of the NVP and EFV bound enzyme using the 1DLO, 1RTH and 1FK9 crystal structures respectively.
Figure 5 Comparison of the squared fluctuations predicted by ANM mode 2 of the NVP bound 1RTH (red) and EFV bound 1FK9 structures (black).
This was based on analysis of the 1RTH NVP bound and 1FK9 EFV bound PDB crystal structures.
Influence of Initial Crystal Structure Choice If the differences observed between the modes seen for 1FK9 and 1RTH is caused by differences in the bound inhibitor, then similar differences should be observed using different EFV and NVP bound structures.
Figure 6 Comparison of the first 15 ANM modes generated from different HIV-1 RT structures bound to NVP and EFV, using the 1RTH and 1VRT NVP bound structures and 1FK9 and 1IKW EFV bound structures.
Publication Year: 2012
Biophysical Insights into the Inhibitory Mechanism of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors.
(2013) Biomolecules 3
PubMed: 24970195 | PubMedCentral: PMC4030976 | DOI: 10.3390/biom3040889
The structures of apo wild-type (WT) RT (left; PDB ID: 1DLO) and WT RT bound to efavirenz (right; PDB ID: 1FK9).
Current perspectives on HIV-1 antiretroviral drug resistance.
(2014) Viruses 6
PubMed: 25341668 | PubMedCentral: PMC4213579 | DOI: 10.3390/v6104095
PDB 1FK9 [ 152 ].
Publication Year: 2014
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