7EKK

Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamideA [auth H]224Homo sapiensMutation(s): 0 
Gene Names: immunoglobin
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamideB [auth L]212Homo sapiensMutation(s): 0 
Gene Names: immunoglobulin
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MPER region of the envelope glycoprotein gp41 from HIV-1C [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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04578
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth H]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth H],
G [auth H],
I [auth L],
J [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth L]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NH4
Query on NH4

Download Ideal Coordinates CCD File 
E [auth H]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.981α = 90
b = 44.8β = 113.63
c = 85.949γ = 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