Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of deoxynucleotide addition by HIV-1 RT during reverse transcription.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 10553, Year 2024
Publish date	Dec 4, 2024
Authors	Sandra Vergara / Xiaohong Zhou / Ulises Santiago / Mounia Alaoui-El-Azher / James F Conway / Nicolas Sluis-Cremer / Guillermo Calero /
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 ...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.
External links	Nat Commun / PubMed:39632888 / PubMed Central
Methods	EM (single particle)
Resolution	2.2 - 3.0 Å
Structure data	43114 8vb6 EMDB-43114, PDB-8vb6: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.7 Å 43115 8vb7 EMDB-43115, PDB-8vb7: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.5 Å 43116 8vb8 EMDB-43116, PDB-8vb8: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 3.0 Å 43117 8vb9 EMDB-43117, PDB-8vb9: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.8 Å 43120 8vbc EMDB-43120, PDB-8vbc: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.8 Å 43121 8vbd EMDB-43121, PDB-8vbd: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.7 Å 43122 8vbe EMDB-43122, PDB-8vbe: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.6 Å 43123 8vbf EMDB-43123, PDB-8vbf: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.8 Å 43124 8vbg EMDB-43124, PDB-8vbg: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.4 Å 43125 8vbh EMDB-43125, PDB-8vbh: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.2 Å 43126 8vbi EMDB-43126, PDB-8vbi: Kinetic intermediate states of HIV-1 RT DNA synthesis captured by cryo-EM Method: EM (single particle) / Resolution: 2.3 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ChemComp-POP: PYROPHOSPHATE 2- ChemComp-F2A: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine ChemComp-UNX: Unknown entry
Source	human immunodeficiency virus 1 synthetic construct (others)
Keywords	TRANSCRIPTION / TRANSFERASE/DNA / Reverse Transcription / Time-resolved / HIV-1 / Cryo-EM / TRANSFERASE-DNA complex