6PYQ

Assembly of VIQKI D455(beta-L-homoaspartic acid)with human parainfluenza virus type 3 (HPIV3) fusion glycoprotein N-terminal heptad repeat domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Effects of Single alpha-to-beta Residue Replacements on Recognition of an Extended Segment in a Viral Fusion Protein.

Outlaw, V.K.Kreitler, D.F.Stelitano, D.Porotto, M.Moscona, A.Gellman, S.H.

(2020) ACS Infect Dis 6: 2017-2022

  • DOI: https://doi.org/10.1021/acsinfecdis.0c00385
  • Primary Citation of Related Structures:  
    6PRL, 6PYQ, 6PZ6, 6V3V, 6VAS

  • PubMed Abstract: 

    Partial replacement of α-amino acid residues with β-amino acid residues has been established as a strategy for preserving target-engagement by helix-forming polypeptides while altering other properties. The impact of β-residue incorporation within polypeptides that adopt less regular conformations, however, has received less attention. The C-terminal heptad repeat (HRC) domains of fusion glycoproteins from pathogenic paramyxoviruses contain a segment that must adopt an extended conformation in order to coassemble with the N-terminal heptad repeat (HRN) domain in the postfusion state and drive a merger of the viral envelope with a target cell membrane. Here, we examine the impact of single α-to-β substitutions within this extended N-terminal segment of an engineered HRC peptide designated VIQKI. Stabilities of hexameric coassemblies formed with the native human parainfluenza virus 3 (HPIV3) HRN have been evaluated, the structures of five coassemblies have been determined, and antiviral efficacies have been measured. Many sites within the extended segment show functional tolerance of α-to-β substitution. These results offer a basis for future development of paramyxovirus infection inhibitors with novel biological activity profiles, possibly including resistance to proteolysis.


  • Organizational Affiliation

    Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion glycoprotein F1
A, C, E
53Human respirovirus 3Mutation(s): 2 
UniProt
Find proteins for P06828 (Human parainfluenza 3 virus (strain Wash/47885/57))
Explore P06828 
Go to UniProtKB:  P06828
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06828
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
synthetic peptide derived from Fusion glycoprotein F1
B, D, F
38Human parainfluenza 3 virus (strain NIH 47885)Mutation(s): 7 
UniProt
Find proteins for P06828 (Human parainfluenza 3 virus (strain Wash/47885/57))
Explore P06828 
Go to UniProtKB:  P06828
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06828
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
B3D
Query on B3D
B, D, F
L-PEPTIDE LINKINGC5 H9 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.85α = 90
b = 49.34β = 103.61
c = 56.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1F32GM122263
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI114736

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-10-21
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection
  • Version 2.1: 2024-07-10
    Changes: Data collection