4F57 | pdb_00004f57

Fab structure of a neutralizing antibody L1 from an early subtype A HIV-1 infected patient


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.186 (Depositor) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4F57

This is version 1.2 of the entry. See complete history

Literature

Viral Escape from Neutralizing Antibodies in Early Subtype A HIV-1 Infection Drives an Increase in Autologous Neutralization Breadth.

Murphy, M.K.Yue, L.Pan, R.Boliar, S.Sethi, A.Tian, J.Pfafferot, K.Karita, E.Allen, S.A.Cormier, E.Goepfert, P.A.Borrow, P.Robinson, J.E.Gnanakaran, S.Hunter, E.Kong, X.P.Derdeyn, C.A.

(2013) PLoS Pathog 9: e1003173-e1003173

  • DOI: https://doi.org/10.1371/journal.ppat.1003173
  • Primary Citation Related Structures: 
    4F57, 4F58

  • PubMed Abstract: 

    Antibodies that neutralize (nAbs) genetically diverse HIV-1 strains have been recovered from a subset of HIV-1 infected subjects during chronic infection. Exact mechanisms that expand the otherwise narrow neutralization capacity observed during early infection are, however, currently undefined. Here we characterized the earliest nAb responses in a subtype A HIV-1 infected Rwandan seroconverter who later developed moderate cross-clade nAb breadth, using (i) envelope (Env) glycoproteins from the transmitted/founder virus and twenty longitudinal nAb escape variants, (ii) longitudinal autologous plasma, and (iii) autologous monoclonal antibodies (mAbs). Initially, nAbs targeted a single region of gp120, which flanked the V3 domain and involved the alpha2 helix. A single amino acid change at one of three positions in this region conferred early escape. One immunoglobulin heavy chain and two light chains recovered from autologous B cells comprised two mAbs, 19.3H-L1 and 19.3H-L3, which neutralized the founder Env along with one or three of the early escape variants carrying these mutations, respectively. Neither mAb neutralized later nAb escape or heterologous Envs. Crystal structures of the antigen-binding fragments (Fabs) revealed flat epitope contact surfaces, where minimal light chain mutation in 19.3H-L3 allowed for additional antigenic interactions. Resistance to mAb neutralization arose in later Envs through alteration of two glycans spatially adjacent to the initial escape signatures. The cross-neutralizing nAbs that ultimately developed failed to target any of the defined V3-proximal changes generated during the first year of infection in this subject. Our data demonstrate that this subject's first recognized nAb epitope elicited strain-specific mAbs, which incrementally acquired autologous breadth, and directed later B cell responses to target distinct portions of Env. This immune re-focusing could have triggered the evolution of cross-clade antibodies and suggests that exposure to a specific sequence of immune escape variants might promote broad humoral responses during HIV-1 infection.


  • Organizational Affiliation
    • Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, Georgia, United States of America.

Macromolecule Content 

  • Total Structure Weight: 47.02 kDa 
  • Atom Count: 3,834 
  • Modeled Residue Count: 438 
  • Deposited Residue Count: 439 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of Fab of a neutralizing antibody L1A [auth L]213Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of Fab of a neutralizing antibody L1B [auth H]226Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth H]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.186 (Depositor) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.101α = 90
b = 57.463β = 112.78
c = 60.038γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary