7B4V

Broadly neutralizing DARPin bnD.2 in complex with the HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization.

Friedrich, N., Stiegeler, E., Glogl, M., Lemmin, T., Hansen, S., Kadelka, C., Wu, Y., Ernst, P., Maliqi, L., Foulkes, C., Morin, M., Eroglu, M., Liechti, T., Ivan, B., Reinberg, T., Schaefer, J.V., Karakus, U., Ursprung, S., Mann, A., Rusert, P., Kouyos, R.D., Robinson, J.A., Gunthard, H.F., Pluckthun, A., Trkola, A.

(2021) Nat Commun 12: 6705-6705

  • DOI: https://doi.org/10.1038/s41467-021-27075-0
  • Primary Citation of Related Structures:  
    7B4T, 7B4U, 7B4V, 7B4W, 7DNE, 7DNF, 7DNG

  • PubMed Abstract: 

    The V3 loop of the HIV-1 envelope (Env) protein elicits a vigorous, but largely non-neutralizing antibody response directed to the V3-crown, whereas rare broadly neutralizing antibodies (bnAbs) target the V3-base. Challenging this view, we present V3-crown directed broadly neutralizing Designed Ankyrin Repeat Proteins (bnDs) matching the breadth of V3-base bnAbs. While most bnAbs target prefusion Env, V3-crown bnDs bind open Env conformations triggered by CD4 engagement. BnDs achieve breadth by focusing on highly conserved residues that are accessible in two distinct V3 conformations, one of which resembles CCR5-bound V3. We further show that these V3-crown conformations can, in principle, be attacked by antibodies. Supporting this conclusion, analysis of antibody binding activity in the Swiss 4.5 K HIV-1 cohort (n = 4,281) revealed a co-evolution of V3-crown reactivities and neutralization breadth. Our results indicate a role of V3-crown responses and its conformational preferences in bnAb development to be considered in preventive and therapeutic approaches.

    • Organizational Affiliation: 

    Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Broadly neutralizing DARPin bnD.2A [auth C],
B [auth A]		132synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)C [auth B],
D		15synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.63α = 90
b = 69.34β = 90
c = 69.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_192689
Swiss National Science FoundationSwitzerland310030B_166676
Swiss National Science FoundationSwitzerland31003A_146278

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references