3IF1 | pdb_00003if1

Crystal structure of 237mAb in complex with a GalNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.285 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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This is version 1.5 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: 94.89 kDa 
  • Atom Count: 6,981 
  • Modeled Residue Count: 850 
  • Deposited Residue Count: 864 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin light chain (IgG2a)
A, C
215Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin heavy chain (IgG2a)
B, D
217Mus musculusMutation(s): 0 

Small Molecules

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

Query on NGA



Download:Ideal Coordinates CCD File
J [auth B],
P [auth D]
2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
K [auth C],
O [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
L [auth C],
M [auth C],
N [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.285 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 279.35α = 90
b = 38.42β = 109.11
c = 95.99γ = 90
Software Package:
Software NamePurpose
d*TREKdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
d*TREKdata scaling

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 1.2: 2011-11-16
    Changes: Atomic model
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-30
    Changes: Structure summary