6HAK

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with a double stranded RNA represents the RT transcription initiation complex prior to nucleotide incorporation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.293 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of HIV-1 RT/dsRNA initiation complex prior to nucleotide incorporation.

Das, K.Martinez, S.E.DeStefano, J.J.Arnold, E.

(2019) Proc.Natl.Acad.Sci.USA 116: 7308-7313

  • DOI: 10.1073/pnas.1814170116

  • PubMed Abstract: 
  • The initiation phase of HIV reverse transcription has features that are distinct from its elongation phase. The first structure of a reverse transcription initiation complex (RTIC) that trapped the complex after incorporation of one ddCMP nucleotide ...

    The initiation phase of HIV reverse transcription has features that are distinct from its elongation phase. The first structure of a reverse transcription initiation complex (RTIC) that trapped the complex after incorporation of one ddCMP nucleotide was published recently [Larsen KP, et al. (2018) Nature 557:118-122]. Here we report a crystal structure of a catalytically active HIV-1 RT/dsRNA complex that mimics the state of the RTIC before the first nucleotide incorporation. The structure reveals that the dsRNA-bound conformation of RT is closer to that of RT bound to a nonnucleoside RT inhibitor (NNRTI) and dsDNA; a hyperextended thumb conformation helps to accommodate the relatively wide dsRNA duplex. The RNA primer 3' end is positioned 5 Å away from the polymerase site; however, unlike in an NNRTI-bound state in which structural elements of RT restrict the movement of the primer, the primer terminus of dsRNA is not blocked from reaching the active site of RT. The observed structural changes and energetic cost of bringing the primer 3' end to the priming site are hypothesized to explain the slower nucleotide incorporation rate of the RTIC. An unusual crystal lattice interaction of dsRNA with its symmetry mate is reminiscent of the RNA architecture within the extended vRNA-tRNA Lys3 in the RTIC. This RT/dsRNA complex captures the key structural characteristics and components of the RTIC, including the RT conformational changes and interactions with the dsRNA primer-binding site region, and these features have implications for better understanding of RT initiation.


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854; kalyan.das@kuleuven.be arnold@cabm.rutgers.edu.,Rega Institute, The Katholieke Universiteit Leuven, 3000 Leuven, Belgium.,Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854.,Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742.,Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854.,Department of Microbiology, Immunology and Transplantation, The Katholieke Universiteit Leuven, 3000 Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag-Pol polyprotein
A, C
556Human 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
Gag-Pol polyprotein
B, D
444Human 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 (5'-R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')T,E23Human immunodeficiency virus 1
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*CP*CP*CP*UP*GP*UP*UP*CP*GP*GP*CP*CP*GP*CP*CP*A)-3')P,F17Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
B
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.293 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 175.240α = 90.00
b = 175.240β = 90.00
c = 225.800γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing
Aimlessdata scaling

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 Allergy and Infectious DiseasesUnited StatesR37 AI027690

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references