6TVW

Structure of native gp41 derived peptide fusion inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.234 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Systematic Evaluation of Fluorination as Modification for Peptide-Based Fusion Inhibitors against HIV-1 Infection.

Huhmann, S.Nyakatura, E.K.Rohrhofer, A.Moschner, J.Schmidt, B.Eichler, J.Roth, C.Koksch, B.

(2021) Chembiochem 22: 3443-3451

  • DOI: https://doi.org/10.1002/cbic.202100417
  • Primary Citation of Related Structures:  
    6TVQ, 6TVU, 6TVW

  • PubMed Abstract: 

    With the emergence of novel viruses, the development of new antivirals is more urgent than ever. A key step in human immunodeficiency virus type 1 (HIV-1) infection is six-helix bundle formation within the envelope protein subunit gp41. Selective disruption of bundle formation by peptides has been shown to be effective; however, these drugs, exemplified by T20, are prone to rapid clearance from the patient. The incorporation of non-natural amino acids is known to improve these pharmacokinetic properties. Here, we evaluate a peptide inhibitor in which a critical Ile residue is replaced by fluorinated analogues. We characterized the influence of the fluorinated analogues on the biophysical properties of the peptide. Furthermore, we show that the fluorinated peptides can block HIV-1 infection of target cells at nanomolar levels. These findings demonstrate that fluorinated amino acids are appropriate tools for the development of novel peptide therapeutics.


  • Organizational Affiliation

    Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Arnimallee 20, 14195, Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinA [auth CCC]38Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q5VGF0 (Human immunodeficiency virus 1)
Explore Q5VGF0 
Go to UniProtKB:  Q5VGF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VGF0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein gp41,Envelope glycoprotein gp160B [auth DbD]31Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for A0A650FAD5 (Human immunodeficiency virus 1)
Explore A0A650FAD5 
Go to UniProtKB:  A0A650FAD5
Find proteins for P04582 (Human immunodeficiency virus type 1 group M subtype B (isolate BH8))
Explore P04582 
Go to UniProtKB:  P04582
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A650FAD5P04582
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.234 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.706α = 90
b = 44.706β = 90
c = 208.857γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
ACORNphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 3.0: 2024-06-26
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary