5B18

Crystal Structure of a Darunavir Resistant HIV-1 Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Unique Flap Conformation in an HIV-1 Protease with High-Level Darunavir Resistance

Nakashima, M.Ode, H.Suzuki, K.Fujino, M.Maejima, M.Kimura, Y.Masaoka, T.Hattori, J.Matsuda, M.Hachiya, A.Yokomaku, Y.Suzuki, A.Watanabe, N.Sugiura, W.Iwatani, Y.

(2016) Front Microbiol 7: 61-61

  • DOI: https://doi.org/10.3389/fmicb.2016.00061
  • Primary Citation of Related Structures:  
    5B18

  • PubMed Abstract: 

    Darunavir (DRV) is one of the most powerful protease inhibitors (PIs) for treating human immunodeficiency virus type-1 (HIV-1) infection and presents a high genetic barrier to the generation of resistant viruses. However, DRV-resistant HIV-1 infrequently emerges from viruses exhibiting resistance to other protease inhibitors. To address this resistance, researchers have gathered genetic information on DRV resistance. In contrast, few structural insights into the mechanism underlying DRV resistance are available. To elucidate this mechanism, we determined the crystal structure of the ligand-free state of a protease with high-level DRV resistance and six DRV resistance-associated mutations (including I47V and I50V), which we generated by in vitro selection. This crystal structure showed a unique curling conformation at the flap regions that was not found in the previously reported ligand-free protease structures. Molecular dynamics simulations indicated that the curled flap conformation altered the flap dynamics. These results suggest that the preference for a unique flap conformation influences DRV binding. These results provide new structural insights into elucidating the molecular mechanism of DRV resistance and aid to develop PIs effective against DRV-resistant viruses.


  • Organizational Affiliation

    Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease
A, B, C, D
99Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for E5RVX9 (Human immunodeficiency virus 1)
Explore E5RVX9 
Go to UniProtKB:  E5RVX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5RVX9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.149α = 89.9
b = 48.699β = 73.98
c = 54.151γ = 86.69
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description