3IET | pdb_00003iet

Crystal Structure of 237mAb with antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.271 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.227 (Depositor) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history

Literature

Antibody recognition of a unique tumor-specific glycopeptide antigen.

Brooks, C.L.Schietinger, A.Borisova, S.N.Kufer, P.Okon, M.Hirama, T.Mackenzie, C.R.Wang, L.X.Schreiber, H.Evans, S.V.

(2010) Proc Natl Acad Sci U S A 107: 10056-10061

  • DOI: https://doi.org/10.1073/pnas.0915176107
  • Primary Citation Related Structures: 
    3IET, 3IF1

  • PubMed Abstract: 

    Aberrant glycosylation and the overexpression of certain carbohydrate moieties is a consistent feature of cancers, and tumor-associated oligosaccharides are actively investigated as targets for immunotherapy. One of the most common aberrations in glycosylation patterns is the presentation of a single O-linked N-acetylgalactosamine on a threonine or serine residue known as the "Tn antigen." Whereas the ubiquitous nature of Tn antigens on cancers has made them a natural focus of vaccine research, such carbohydrate moieties are not always tumor-specific and have been observed on embryonic and nonmalignant adult tissue. Here we report the structural basis of binding of a complex of a monoclonal antibody (237mAb) with a truly tumor-specific glycopeptide containing the Tn antigen. In contrast to glycopeptide-specific antibodies in complex with simple peptides, 237mAb does not recognize a conformational epitope induced in the peptide by sugar substitution. Instead, 237mAb uses a pocket coded by germ-line genes to completely envelope the carbohydrate moiety itself while interacting with the peptide moiety in a shallow groove. Thus, 237mAb achieves its striking tumor specificity, with no observed physiological cross-reactivity to the unglycosylated peptide or the free glycan, by a combination of multiple weak but specific interactions to both the peptide and to the glycan portions of the antigen.


  • Organizational Affiliation
    • Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8P 3P6.

Macromolecule Content 

  • Total Structure Weight: 97.4 kDa 
  • Atom Count: 7,204 
  • Modeled Residue Count: 868 
  • Deposited Residue Count: 888 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin light chain (IgG2a)
A, C
217Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin heavy chain (IgG2a)
B, D
218Mus musculusMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PodoplaninE [auth X],
F [auth Q]
9Mus musculusMutation(s): 0 
Gene Names: PdpnRP23-348F1.2-002
UniProt & NIH Common Fund Data Resources
Find proteins for Q62011 (Mus musculus)
Explore Q62011 
Go to UniProtKB:  Q62011
IMPC:  MGI:103098
Entity Groups
UniProt GroupQ62011
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q62011-1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.271 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.227 (Depositor) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 277.91α = 90
b = 38.24β = 108.99
c = 95.91γ = 90
Software Package:
Software NamePurpose
d*TREKdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary