6P2G

Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and D-ddCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine.

Bertoletti, N.Chan, A.H.Schinazi, R.F.Yin, Y.W.Anderson, K.S.

(2019) Protein Sci. 28: 1664-1675

  • DOI: 10.1002/pro.3681
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The retrovirus HIV-1 has been a major health issue since its discovery in the early 80s. In 2017, over 37 million people were infected with HIV-1, of which 1.8 million were new infections that year. Currently, the most successful treatment regimen is ...

    The retrovirus HIV-1 has been a major health issue since its discovery in the early 80s. In 2017, over 37 million people were infected with HIV-1, of which 1.8 million were new infections that year. Currently, the most successful treatment regimen is the highly active anti-retroviral therapy (HAART), which consists of a combination of three to four of the current 26 FDA-approved HIV-1 drugs. Half of these drugs target the reverse transcriptase (RT) enzyme that is essential for viral replication. One class of RT inhibitors are nucleoside reverse transcriptase inhibitors (NRTIs), a crucial component of the HAART therapy. Once incorporated into DNA, NRTIs function as a chain terminator to stop viral DNA replication. Unfortunately, treatment with NRTIs is sometimes linked to toxicity caused by off-target side effects. NRTIs may also target the replicative human mitochondrial DNA polymerase (Pol γ), causing long-term severe drug toxicity. The goal of this work is to understand the discrimination mechanism of different NRTI analogs by RT. Crystal structures and kinetic experiments are essential for the rational design of new molecules that are able to bind selectively to RT and not Pol γ. Structural comparison of NRTI-binding modes with both RT and Pol γ enzymes highlights key amino acids that are responsible for the difference in affinity of these drugs to their targets. Therefore, the long-term goal of this research is to develop safer, next generation therapeutics that can overcome off-target toxicity. This article is protected by copyright. All rights reserved.


    Organizational Affiliation

    Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA.,Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06520-8066, USA.,Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, 77555, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520-8066, USA.,Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
A
560Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 2 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
p51 RT
B
452Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Entity ID: 3
MoleculeChainsLengthOrganism
DNA Primer 20-merP21synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA template 27-merT27synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
P, T
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DCT
Query on DCT

Download SDF File 
Download CCD File 
A
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
G47
Query on G47
P
DNA LINKINGC12 H18 N5 O7 P SDG
DDG
Query on DDG
P
DNA LINKINGC10 H14 N5 O6 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 168.548α = 90.00
b = 171.578β = 90.00
c = 106.001γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

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 StatesGM049551

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection, Database references
  • Version 1.2: 2019-08-28
    Type: Data collection, Database references
  • Version 1.3: 2020-01-01
    Type: Author supporting evidence