7UEL | pdb_00007uel

Genetic and structural basis for the human anti-alpha-galactosyl antibody response


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.215 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7UEL

This is version 1.4 of the entry. See complete history

Literature

Genetic and structural basis of the human anti-alpha-galactosyl antibody response.

Langley, D.B.Schofield, P.Nevoltris, D.Jackson, J.Jackson, K.J.L.Peters, T.J.Burk, M.Matthews, J.M.Basten, A.Goodnow, C.C.van Nunen, S.Reed, J.H.Christ, D.

(2022) Proc Natl Acad Sci U S A 119: e2123212119-e2123212119

  • DOI: https://doi.org/10.1073/pnas.2123212119
  • Primary Citation Related Structures: 
    7UEL, 7UEM, 7UEN

  • PubMed Abstract: 

    Humans lack the capacity to produce the Galα1-3Galβ1-4GlcNAc (α-gal) glycan, and produce anti-α-gal antibodies upon exposure to the carbohydrate on a diverse set of immunogens, including commensal gut bacteria, malaria parasites, cetuximab, and tick proteins. Here we use X-ray crystallographic analysis of antibodies from α-gal knockout mice and humans in complex with the glycan to reveal a common binding motif, centered on a germline-encoded tryptophan residue at Kabat position 33 (W33) of the complementarity-determining region of the variable heavy chain (CDRH1). Immunoglobulin sequencing of anti-α-gal B cells in healthy humans and tick-induced mammalian meat anaphylaxis patients revealed preferential use of heavy chain germline IGHV3-7, encoding W33, among an otherwise highly polyclonal antibody response. Antigen binding was critically dependent on the presence of the germline-encoded W33 residue for all of the analyzed antibodies; moreover, introduction of the W33 motif into naive IGHV3-23 antibody phage libraries enabled the rapid selection of α-gal binders. Our results outline structural and genetic factors that shape the human anti-α-galactosyl antibody response, and provide a framework for future therapeutics development.


  • Organizational Affiliation
    • Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.

Macromolecule Content 

  • Total Structure Weight: 47.62 kDa 
  • Atom Count: 3,602 
  • Modeled Residue Count: 433 
  • Deposited Residue Count: 443 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain Fab of antibody JEC1A [auth H]229Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain Fab of antibody JEC1B [auth L]214Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
F [auth L]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth H]
D [auth H]
E [auth H]
G [auth L]
H [auth L]
C [auth H],
D [auth H],
E [auth H],
G [auth L],
H [auth L],
I [auth L]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
J [auth L]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.215 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.54α = 90
b = 71.37β = 104.94
c = 95.821γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references
  • Version 1.2: 2022-08-03
    Changes: Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary