6IK9

HIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:DNA:dGTP ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.435 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified nucleoside RT inhibitors.

Yasutake, Y.Hattori, S.I.Tamura, N.Matsuda, K.Kohgo, S.Maeda, K.Mitsuya, H.

(2019) Biochem. Biophys. Res. Commun. 509: 943-948

  • DOI: 10.1016/j.bbrc.2019.01.026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleoside analogue reverse transcriptase (RT) inhibitors (NRTIs) are major antiviral agents against hepatitis B virus (HBV) and human immunodeficiency virus type-1 (HIV-1). However, the notorious insoluble property of HBV RT has prevented atomic-res ...

    Nucleoside analogue reverse transcriptase (RT) inhibitors (NRTIs) are major antiviral agents against hepatitis B virus (HBV) and human immunodeficiency virus type-1 (HIV-1). However, the notorious insoluble property of HBV RT has prevented atomic-resolution structural studies and rational anti-HBV drug design. Here, we created HIV-1 RT mutants containing HBV-mimicking sextuple or septuple amino acid substitutions at the nucleoside-binding site (N-site) and verified that these mutants retained the RT activity. The most active RT mutant, HIV-1 RT 7MC , carrying Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L was successfully crystallized, and its three-dimensional structure was determined in complex with DNA:dGTP/entecavir-triphosphate (ETV-TP), a potent anti-HBV guanosine analogue RT inhibitor, at a resolution of 2.43 Å and 2.60 Å, respectively. The structures reveal significant positional rearrangements of the amino acid side-chains at the N-site, elucidating the mechanism underlying the differential susceptibility of HIV-1 and HBV against recently reported 4'-modified NRTIs.


    Organizational Affiliation

    National Center for Global Health and Medicine Research Institute (NCGM), Tokyo, 162-8655, Japan.,National Center for Global Health and Medicine Research Institute (NCGM), Tokyo, 162-8655, Japan. Electronic address: kmaeda@ri.ncgm.go.jp.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Sapporo, 062-8517, Japan. Electronic address: y-yasutake@aist.go.jp.,National Center for Global Health and Medicine Research Institute (NCGM), Tokyo, 162-8655, Japan; Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, 860-0082, Japan.,National Center for Global Health and Medicine Research Institute (NCGM), Tokyo, 162-8655, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA; Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto, 860-8556, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 reverse transcriptase p66 subunit
A, C
557Human immunodeficiency virus 1Mutation(s): 9 
Gene Names: pol
Find proteins for D3XFN7 (Human immunodeficiency virus 1)
Go to UniProtKB:  D3XFN7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 reverse transcriptase p51 subunit
B, D
444Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 2 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
Entity ID: 3
MoleculeChainsLengthOrganism
DNA/RNA (38-MER)E,F38synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DGT
Query on DGT

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Download CCD File 
A, F
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMC
Query on OMC
E, F
RNA LINKINGC10 H16 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.435 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 284.869α = 90.00
b = 284.869β = 90.00
c = 95.892γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP18fk0310113

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references