7EKB

Crystal structure of 4E10 modified with pyrene acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.121 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile.

Rujas, E.Leaman, D.P.Insausti, S.Carravilla, P.Garcia-Porras, M.Largo, E.Morillo, I.Sanchez-Eugenia, R.Zhang, L.Cui, H.Iloro, I.Elortza, F.Julien, J.P.Eggeling, C.Zwick, M.B.Caaveiro, J.M.M.Nieva, J.L.

(2021) iScience 24: 102987-102987

  • DOI: https://doi.org/10.1016/j.isci.2021.102987
  • Primary Citation of Related Structures:  
    7EKB, 7EKK

  • PubMed Abstract: 

    Broadly neutralizing antibodies (bnAbs) against HIV-1 are frequently associated with the presence of autoreactivity/polyreactivity, a property that can limit their use as therapeutic agents. The bnAb 4E10, targeting the conserved Membrane proximal external region (MPER) of HIV-1, displays almost pan-neutralizing activity across globally circulating HIV-1 strains but exhibits nonspecific off-target interactions with lipid membranes. The hydrophobic apex of the third complementarity-determining region of the heavy chain (CDRH3) loop, which is essential for viral neutralization, critically contributes to this detrimental effect. Here, we have replaced the aromatic/hydrophobic residues from the apex of the CDRH3 of 4E10 with a single aromatic molecule through chemical modification to generate a variant that preserves the neutralization potency and breadth of 4E10 but with reduced autoreactivity. Collectively, our study suggests that the localized accumulation of aromaticity by chemical modification provides a pathway to ameliorate the adverse effects triggered by the CDRH3 of anti-HIV-1 MPER bnAbs.


  • Organizational Affiliation

    Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab region of the heavy chain of broadly neutralizing antibody anti-HIV-1 4E10A [auth H]228Homo sapiensMutation(s): 0 
Gene Names: Immunoglobulin
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab region of the light chain of the broadly neutralizing anti-HIV-1 antibody 4E10B [auth L]214Homo sapiensMutation(s): 0 
Gene Names: Immunoglobulin
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MPER region of the HIV-1 envelope glycoprotein protein gp41C [auth P]16Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04578 
Go to UniProtKB:  P04578
Entity Groups  
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UniProt GroupP04578
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.121 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.109α = 90
b = 44.89β = 113.68
c = 86.041γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description