8VB9

Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM

Summary for 8VB9

• Entry DOI: 10.2210/pdb8vb9/pdb
• EMDB information: 43117
• Descriptor: HIV-1 reverse transcriptase/ribonuclease H P66 subunit, HIV-1 reverse transcriptase P51 subunit, DNA (38-MER), ... (5 entities in total)
• Functional Keywords: reverse transcription, time-resolved, hiv-1, cryo-em, transcription, transferase-dna complex, transferase/dna
• Biological source: Human immunodeficiency virus 1; More
• Total number of polymer chains: 3
• Total formula weight: 128328.45

Authors

Vergara, S.,Zhou, X.,Santiago, U.,Conway, J.F.,Sluis-Cremer, N.,Calero, G. (deposition date: 2023-12-12, release date: 2024-12-11, Last modification date: 2024-12-18)

Primary citation

Vergara, S.,Zhou, X.,Santiago, U.,Alaoui-El-Azher, M.,Conway, J.F.,Sluis-Cremer, N.,Calero, G.
Structural basis of deoxynucleotide addition by HIV-1 RT during reverse transcription.
Nat Commun, 15:10553-10553, 2024

PubMed Abstract: Reverse transcription of the retroviral RNA genome into DNA is an integral step during HIV-1 replication. Despite a wealth of structural information on reverse transcriptase (RT), we lack insight into the intermediate states of DNA synthesis. Using catalytically active substrates, and a blot/diffusion cryo-electron microscopy approach, we capture 11 structures encompassing reactant, intermediate and product states of dATP addition by RT at 2.2 to 3.0 Å resolution. In the reactant state, dATP binding to RT-template/primer involves a single Mg (site B) inducing formation of a negatively charged pocket where a second floating Mg can bind (site A). During the intermediate state, the α-phosphate oxygen from a previously unobserved dATP conformer aligns with site A Mg and the primer 3'-OH for nucleophilic attack. The product state, comprises two substrate conformations including an incorporated dAMP with the pyrophosphate leaving group coordinated by metal B and stabilized through H-bonds. Moreover, K220 mutants significantly impact the rate of dNTP incorporation by RT and HIV-1 replication capacity. This work sheds light into the dynamic components of a reaction that is central to HIV-1 replication.

PubMed: 39632888
DOI: 10.1038/s41467-024-54618-y

Experimental method

ELECTRON MICROSCOPY (2.8 Å)