7P15

Cryo-EM structure of HIV-1 reverse transcriptase with a DNA aptamer in complex with fragment F04 at the transient P-pocket

Summary for 7P15

• Entry DOI: 10.2210/pdb7p15/pdb
• Related: 7OZW
• EMDB information: 13139 13156
• Descriptor: Reverse transcriptase/ribonuclease H, DNA (37-MER), (1~{R},2~{R})-~{N}-(1~{H}-pyrazol-4-yl)-2-pyridin-3-yl-cyclopropane-1-carboxamide, ... (4 entities in total)
• Functional Keywords: reverse transcriptase, rt-aptamer complex, rt sliding, p-1 complex, p51, p66, transferase
• Biological source: Human immunodeficiency virus type 1 BH10 (HIV-1); More
• Total number of polymer chains: 3
• Total formula weight: 125749.47

Authors

Singh, A.K.,Das, K. (deposition date: 2021-07-01, release date: 2021-12-08, Last modification date: 2024-11-13)

Primary citation

Singh, A.K.,Martinez, S.E.,Gu, W.,Nguyen, H.,Schols, D.,Herdewijn, P.,De Jonghe, S.,Das, K.
Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening.
Nat Commun, 12:7127-7127, 2021

PubMed Abstract: HIV-1 reverse transcriptase (RT) slides over an RNA/DNA or dsDNA substrate while copying the viral RNA to a proviral DNA. We report a crystal structure of RT/dsDNA complex in which RT overstepped the primer 3'-end of a dsDNA substrate and created a transient P-pocket at the priming site. We performed a high-throughput screening of 300 drug-like fragments by X-ray crystallography that identifies two leads that bind the P-pocket, which is composed of structural elements from polymerase active site, primer grip, and template-primer that are resilient to drug-resistance mutations. Analogs of a fragment were synthesized, two of which show noticeable RT inhibition. An engineered RT/DNA aptamer complex could trap the transient P-pocket in solution, and structures of the RT/DNA complex were determined in the presence of an inhibitory fragment. A synthesized analog bound at P-pocket is further analyzed by single-particle cryo-EM. Identification of the P-pocket within HIV RT and the developed structure-based platform provide an opportunity for the design new types of polymerase inhibitors.

PubMed: 34880240
DOI: 10.1038/s41467-021-27409-y

Experimental method

ELECTRON MICROSCOPY (3.58 Å)