7Z7C

Broadly neutralizing DARPin bnD.8 in complex with the HIV-1 envelope variable loop 3 peptide V3 (BF520)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization.

Glogl, M.Friedrich, N.Cerutti, G.Lemmin, T.Kwon, Y.D.Gorman, J.Maliqi, L.Mittl, P.R.E.Hesselman, M.C.Schmidt, D.Weber, J.Foulkes, C.Dingens, A.S.Bylund, T.Olia, A.S.Verardi, R.Reinberg, T.Baumann, N.S.Rusert, P.Dreier, B.Shapiro, L.Kwong, P.D.Pluckthun, A.Trkola, A.

(2023) Nat Struct Mol Biol 30: 1323-1336

  • DOI: https://doi.org/10.1038/s41594-023-01062-z
  • Primary Citation of Related Structures:  
    7TXD, 7Z7C, 8AED

  • PubMed Abstract: 

    The third variable (V3) loop on the human immunodeficiency virus 1 (HIV-1) envelope glycoprotein trimer is indispensable for virus cell entry. Conformational masking of V3 within the trimer allows efficient neutralization via V3 only by rare, broadly neutralizing glycan-dependent antibodies targeting the closed prefusion trimer but not by abundant antibodies that access the V3 crown on open trimers after CD4 attachment. Here, we report on a distinct category of V3-specific inhibitors based on designed ankyrin repeat protein (DARPin) technology that reinstitute the CD4-bound state as a key neutralization target with up to >90% breadth. Broadly neutralizing DARPins (bnDs) bound V3 solely on open envelope and recognized a four-turn amphipathic α-helix in the carboxy-terminal half of V3 (amino acids 314-324), which we termed 'αV3C'. The bnD contact surface on αV3C was as conserved as the CD4 binding site. Molecular dynamics and escape mutation analyses underscored the functional relevance of αV3C, highlighting the potential of αV3C-based inhibitors and, more generally, of postattachment inhibition of HIV-1.


  • Organizational Affiliation

    Institute for 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.8162synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp16022Human immunodeficiency virus 1Mutation(s): 6 
UniProt
Find proteins for Q9Q714 (Human immunodeficiency virus type 1 group M subtype H (isolate VI991))
Explore Q9Q714 
Go to UniProtKB:  Q9Q714
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Q714
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.227α = 90
b = 40.602β = 113.91
c = 45.631γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.2: 2023-08-30
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Database references
  • Version 1.4: 2024-02-07
    Changes: Refinement description