6PSA

PIE12 D-PEPTIDE AGAINST HIV ENTRY (IN COMPLEX WITH IQN17 Q577R RESISTANCE MUTANT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Characterization of resistance to a potent D-peptide HIV entry inhibitor.

Smith, A.R.Weinstock, M.T.Siglin, A.E.Whitby, F.G.Francis, J.N.Hill, C.P.Eckert, D.M.Root, M.J.Kay, M.S.

(2019) Retrovirology 16: 28-28

  • DOI: https://doi.org/10.1186/s12977-019-0489-7
  • Primary Citation of Related Structures:  
    6PSA

  • PubMed Abstract: 

    PIE12-trimer is a highly potent D-peptide HIV-1 entry inhibitor that broadly targets group M isolates. It specifically binds the three identical conserved hydrophobic pockets at the base of the gp41 N-trimer with sub-femtomolar affinity. This extremely high affinity for the transiently exposed gp41 trimer provides a reserve of binding energy (resistance capacitor) to prevent the viral resistance pathway of stepwise accumulation of modest affinity-disrupting mutations. Such modest mutations would not affect PIE12-trimer potency and therefore not confer a selective advantage. Viral passaging in the presence of escalating PIE12-trimer concentrations ultimately selected for PIE12-trimer resistant populations, but required an extremely extended timeframe (> 1 year) in comparison to other entry inhibitors. Eventually, HIV developed resistance to PIE12-trimer by mutating Q577 in the gp41 pocket.


  • Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PIE12 D-peptideA [auth H]18synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IQN17B [auth A]47Saccharomyces cerevisiaeHuman immunodeficiency virus 1
This entity is chimeric
Mutation(s): 3 
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03069 
Go to UniProtKB:  P03069
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04578 
Go to UniProtKB:  P04578
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP03069P04578
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
B [auth A]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.180 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.843α = 90
b = 48.843β = 90
c = 67.634γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release