6KDM

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:entecavir 5'-triphosphate ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.

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

(2020) Sci Rep 10: 3021-3021

  • DOI: 10.1038/s41598-020-59775-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chronic hepatitis B virus (HBV) infection is a major public health problem that affects millions of people worldwide. Nucleoside analogue reverse transcriptase (RT) inhibitors, such as entecavir (ETV) and lamivudine (3TC), serve as crucial anti-HBV d ...

    Chronic hepatitis B virus (HBV) infection is a major public health problem that affects millions of people worldwide. Nucleoside analogue reverse transcriptase (RT) inhibitors, such as entecavir (ETV) and lamivudine (3TC), serve as crucial anti-HBV drugs. However, structural studies of HBV RT have been hampered due to its unexpectedly poor solubility. Here, we show that human immunodeficiency virus type-1 (HIV-1) with HBV-associated amino acid substitutions Y115F/F116Y/Q151M in its RT (HIV Y115F/F116Y/Q151M ) is highly susceptible to ETV and 3TC. Additionally, we experimentally simulated previously reported ETV/3TC resistance for HBV using HIV Y115F/F116Y/Q151M with F160M/M184V (L180M/M204V in HBV RT) substituted. We determined crystal structures for HIV-1 RT Y115F/F116Y/Q151M :DNA complexed with 3TC-triphosphate (3TC-TP)/ETV-triphosphate (ETV-TP)/dCTP/dGTP. These structures revealed an atypically tight binding conformation of 3TC-TP, where the Met184 side-chain is pushed away by the oxathiolane of 3TC-TP and exocyclic methylene of ETV-TP. Structural analysis of RT Y115F/F116Y/Q151M/F160M/M184V :DNA:3TC-TP also demonstrated that the loosely bound 3TC-TP is misaligned at the active site to prevent a steric clash with the side chain γ-methyl of Val184. These findings shed light on the common structural mechanism of HBV and HIV-1 resistance to 3TC and ETV and should aid in the design of new agents to overcome drug resistance to 3TC and ETV.


    Organizational Affiliation

    Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, 169-8555, Japan. y-yasutake@aist.go.jp.,National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.,National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan. kmaeda@ri.ncgm.go.jp.,Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto, 860-8556, Japan.,Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, 860-0082, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan. y-yasutake@aist.go.jp.




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): 5 
Gene Names: pol
Find proteins for D3XFN5 (Human immunodeficiency virus 1)
Go to UniProtKB:  D3XFN5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 RT 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
ET9
Query on ET9

Download SDF File 
Download CCD File 
A, C
[[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
Entecavir 5'-triphosphate
C12 H18 N5 O12 P3
YMBBDUCQYPKKJK-FXQIFTODSA-N
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-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: 2.32 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 284.447α = 90.00
b = 284.447β = 90.00
c = 95.773γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHENIXphasing
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)JapanJP19fk0310113

Revision History 

  • Version 1.0: 2020-03-04
    Type: Initial release