7Z2G

Cryo-EM structure of HIV-1 reverse transcriptase with a DNA aptamer in complex with doravirine

Summary for 7Z2G

• Entry DOI: 10.2210/pdb7z2g/pdb
• Related: 7Z24 7Z29 7Z2D 7Z2E
• EMDB information: 14457 14458 14462 14463 14465
• Descriptor: Reverse transcriptase/ribonuclease H, DNA (38-MER), 3-chloro-5-({1-[(4-methyl-5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)methyl]-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl}oxy)benzonitrile, ... (4 entities in total)
• Functional Keywords: reverse transcriptase, rt-aptamer complex, non-nucleoside inhibitor, nnrti, transferase
• Biological source: Human immunodeficiency virus type 1 BH10; More
• Total number of polymer chains: 3
• Total formula weight: 126242.13

Authors

Singh, A.K.,Das, K. (deposition date: 2022-02-26, release date: 2022-07-20, Last modification date: 2024-07-17)

Primary citation

Singh, A.K.,De Wijngaert, B.,Bijnens, M.,Uyttersprot, K.,Nguyen, H.,Martinez, S.E.,Schols, D.,Herdewijn, P.,Pannecouque, C.,Arnold, E.,Das, K.
Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine.
Proc.Natl.Acad.Sci.USA, 119:e2203660119-e2203660119, 2022

PubMed Abstract: Structures trapping a variety of functional and conformational states of HIV-1 reverse transcriptase (RT) have been determined by X-ray crystallography. These structures have played important roles in explaining the mechanisms of catalysis, inhibition, and drug resistance and in driving drug design. However, structures of several desired complexes of RT could not be obtained even after many crystallization or crystal soaking experiments. The ternary complexes of doravirine and rilpivirine with RT/DNA are such examples. Structural study of HIV-1 RT by single-particle cryo-electron microscopy (cryo-EM) has been challenging due to the enzyme's relatively smaller size and higher flexibility. We optimized a protocol for rapid structure determination of RT complexes by cryo-EM and determined six structures of wild-type and E138K/M184I mutant RT/DNA in complexes with the nonnucleoside inhibitors rilpivirine, doravirine, and nevirapine. RT/DNA/rilpivirine and RT/DNA/doravirine complexes have structural differences between them and differ from the typical conformation of nonnucleoside RT inhibitor (NNRTI)-bound RT/double-stranded DNA (dsDNA), RT/RNA-DNA, and RT/dsRNA complexes; the primer grip in RT/DNA/doravirine and the YMDD motif in RT/DNA/rilpivirine have large shifts. The DNA primer 3'-end in the doravirine-bound structure is positioned at the active site, but the complex is in a nonproductive state. In the mutant RT/DNA/rilpivirine structure, I184 is stacked with the DNA such that their relative positioning can influence rilpivirine in the pocket. Simultaneously, E138K mutation opens the NNRTI-binding pocket entrance, potentially contributing to a faster rate of rilpivirine dissociation by E138K/M184I mutant RT, as reported by an earlier kinetic study. These structural differences have implications for understanding molecular mechanisms of drug resistance and for drug design.

PubMed: 35858448
DOI: 10.1073/pnas.2203660119

Experimental method

ELECTRON MICROSCOPY (3.65 Å)