5N7B

Understanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Design of Potent Tumor-Associated Antigens: Modulation of Peptide Presentation by Single-Atom O/S or O/Se Substitutions at the Glycosidic Linkage.

Companon, I.Guerreiro, A.Mangini, V.Castro-Lopez, J.Escudero-Casao, M.Avenoza, A.Busto, J.H.Castillon, S.Jimenez-Barbero, J.Asensio, J.L.Jimenez-Oses, G.Boutureira, O.Peregrina, J.M.Hurtado-Guerrero, R.Fiammengo, R.Bernardes, G.J.L.Corzana, F.

(2019) J.Am.Chem.Soc. 141: 4063-4072

  • DOI: 10.1021/jacs.8b13503
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GalNAc-glycopeptides derived from mucin MUC1 are an important class of tumor-associated antigens. α- O-glycosylation forces the peptide to adopt an extended conformation in solution, which is far from the structure observed in complexes with a model ...

    GalNAc-glycopeptides derived from mucin MUC1 are an important class of tumor-associated antigens. α- O-glycosylation forces the peptide to adopt an extended conformation in solution, which is far from the structure observed in complexes with a model anti-MUC1 antibody. Herein, we propose a new strategy for designing potent antigen mimics based on modulating peptide/carbohydrate interactions by means of O → S/Se replacement at the glycosidic linkage. These minimal chemical modifications bring about two key structural changes to the glycopeptide. They increase the carbohydrate-peptide distance and change the orientation and dynamics of the glycosidic linkage. As a result, the peptide acquires a preorganized and optimal structure suited for antibody binding. Accordingly, these new glycopeptides display improved binding toward a representative anti-MUC1 antibody relative to the native antigens. To prove the potential of these glycopeptides as tumor-associated MUC1 antigen mimics, the derivative bearing the S-glycosidic linkage was conjugated to gold nanoparticles and tested as an immunogenic formulation in mice without any adjuvant, which resulted in a significant humoral immune response. Importantly, the mice antisera recognize cancer cells in biopsies of breast cancer patients with high selectivity. This finding demonstrates that the antibodies elicited against the mimetic antigen indeed recognize the naturally occurring antigen in its physiological context. Clinically, the exploitation of tumor-associated antigen mimics may contribute to the development of cancer vaccines and to the improvement of cancer diagnosis based on anti-MUC1 antibodies. The methodology presented here is of general interest for applications because it may be extended to modulate the affinity of biologically relevant glycopeptides toward their receptors.


    Organizational Affiliation

    CIC bioGUNE , Bizkaia Technology Park , Building 801A , 48170 Derio , Spain.,Department of Organic Chemistry II, Faculty of Science & Technology , University of the Basque Country , 48940 Leioa , Spain.,Instituto de Medicina Molecular, Faculdade de Medicina , Universidade de Lisboa , Avenida Professor Egas Moniz , 1649-028 Lisboa , Portugal.,Instituto de Química Orgánica General , IQOG-CSIC , 28006 Madrid , Spain.,Departamento de Química , Universidad de La Rioja , Centro de Investigación en Síntesis Química , 26006 Logroño , Spain.,Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW Cambridge , U.K.,Center for Biomolecular Nanotechnologies@UniLe , Istituto Italiano di Tecnologia (IIT) , 73010 Arnesano , Lecce , Italy.,Ikerbasque , Basque Foundation for Science , Maria Diaz de Haro 13 , 48009 Bilbao , Spain.,Institute of Biocomputation and Physics of Complex Systems (BIFI) , University of Zaragoza , BIFI-IQFR (CSIC), Fundación ARAID , 50018 Zaragoza , Spain.,Departament de Química Analítica i Química Orgànica, Facultat de Química , Universitat Rovira i Virgili , 43007 Tarragona , Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ig heavy chain V-III region J606,Ig lambda-1 chain V region S43
H
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
APD(CG6)RP(NH2) peptide
I
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
I
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
I
NON-POLYMERH2 N

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CG6
Query on CG6
I
L-peptide linkingC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.403α = 90.00
b = 68.648β = 90.00
c = 90.917γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spain--

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references