6B19

Architecture of HIV-1 reverse transcriptase initiation complex core


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Architecture of an HIV-1 reverse transcriptase initiation complex.

Larsen, K.P.Mathiharan, Y.K.Kappel, K.Coey, A.T.Chen, D.H.Barrero, D.Madigan, L.Puglisi, J.D.Skiniotis, G.Puglisi, E.V.

(2018) Nature 557: 118-122

  • DOI: 10.1038/s41586-018-0055-9

  • PubMed Abstract: 
  • Reverse transcription of the HIV-1 RNA genome into double-stranded DNA is a central step in viral infection <sup>1 </sup> and a common target of antiretroviral drugs <sup>2 </sup> . The reaction is catalysed by viral reverse transcriptase (RT) <sup ...

    Reverse transcription of the HIV-1 RNA genome into double-stranded DNA is a central step in viral infection 1 and a common target of antiretroviral drugs 2 . The reaction is catalysed by viral reverse transcriptase (RT) 3,4 that is packaged in an infectious virion with two copies of viral genomic RNA 5 each bound to host lysine 3 transfer RNA (tRNA Lys 3 ), which acts as a primer for initiation of reverse transcription 6,7 . Upon viral entry into cells, initiation is slow and non-processive compared to elongation 8,9 . Despite extensive efforts, the structural basis of RT function during initiation has remained a mystery. Here we use cryo-electron microscopy to determine a three-dimensional structure of an HIV-1 RT initiation complex. In our structure, RT is in an inactive polymerase conformation with open fingers and thumb and with the nucleic acid primer-template complex shifted away from the active site. The primer binding site (PBS) helix formed between tRNA Lys 3 and HIV-1 RNA lies in the cleft of RT and is extended by additional pairing interactions. The 5' end of the tRNA refolds and stacks on the PBS to create a long helical structure, while the remaining viral RNA forms two helical stems positioned above the RT active site, with a linker that connects these helices to the RNase H region of the PBS. Our results illustrate how RNA structure in the initiation complex alters RT conformation to decrease activity, highlighting a potential target for drug action.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. epuglisi@stanford.edu.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Program in Biophysics, Stanford University, Stanford, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
reverse transcriptase p66 subunit
A
570Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 3 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
reverse transcriptase p51 subunit
B
442Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Entity ID: 3
MoleculeChainsLengthOrganism
RNA genome fragmentC101Human immunodeficiency virus 1
Entity ID: 4
MoleculeChainsLengthOrganism
tRNA lysine3D77Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM082545

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references
  • Version 1.2: 2020-01-01
    Type: Author supporting evidence