7Z2G

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

7Z2G の概要

• エントリーDOI: 10.2210/pdb7z2g/pdb
• 関連するPDBエントリー: 7Z24 7Z29 7Z2D 7Z2E
• EMDBエントリー: 14457 14458 14462 14463 14465
• 分子名称: 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)
• 機能のキーワード: reverse transcriptase, rt-aptamer complex, non-nucleoside inhibitor, nnrti, transferase
• 由来する生物種: Human immunodeficiency virus type 1 BH10; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 126242.13

構造登録者

Singh, A.K.,Das, K. (登録日: 2022-02-26, 公開日: 2022-07-20, 最終更新日: 2024-07-17)

主引用文献

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

実験手法

ELECTRON MICROSCOPY (3.65 Å)