6TGG

scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Synthesis, conformational analysis and in vivo assays of an anti-cancer vaccine that features an unnatural antigen based on an sp 2 -iminosugar fragment.

Bermejo, I.A., Navo, C.D., Castro-Lopez, J., Guerreiro, A., Jimenez-Moreno, E., Sanchez Fernandez, E.M., Garcia-Martin, F., Hinou, H., Nishimura, S.I., Garcia Fernandez, J.M., Mellet, C.O., Avenoza, A., Busto, J.H., Bernardes, G.J.L., Hurtado-Guerrero, R., Peregrina, J.M., Corzana, F.

(2020) Chem Sci 11: 3996-4006

  • DOI: 10.1039/c9sc06334j
  • Primary Citation of Related Structures:  
    6TGG

  • PubMed Abstract: 

    • The Tn antigen (GalNAc-α-1- O -Thr/Ser) is a well-known tumor-associated carbohydrate determinant. The use of glycopeptides that incorporate this structure has become a significant and promising niche of research owing to their potential use as anticancer vaccines ...

    The Tn antigen (GalNAc-α-1- O -Thr/Ser) is a well-known tumor-associated carbohydrate determinant. The use of glycopeptides that incorporate this structure has become a significant and promising niche of research owing to their potential use as anticancer vaccines. Herein, the conformational preferences of a glycopeptide with an unnatural Tn antigen, characterized by a threonine decorated with an sp 2 -iminosugar-type α-GalNAc mimic, have been studied both in solution, by combining NMR spectroscopy and molecular dynamics simulations, and in the solid state bound to an anti-mucin-1 (MUC1) antibody, by X-ray crystallography. The Tn surrogate can mimic the main conformer sampled by the natural antigen in solution and exhibits high affinity towards anti-MUC1 antibodies. Encouraged by these data, a cancer vaccine candidate based on this unnatural glycopeptide and conjugated to the carrier protein Keyhole Limpet Hemocyanin (KLH) has been prepared and tested in mice. Significantly, the experiments in vivo have proved that this vaccine elicits higher levels of specific anti-MUC1 IgG antibodies than the analog that bears the natural Tn antigen and that the elicited antibodies recognize human breast cancer cells with high selectivity. Altogether, we compile evidence to confirm that the presentation of the antigen, both in solution and in the bound state, plays a critical role in the efficacy of the designed cancer vaccines. Moreover, the outcomes derived from this vaccine prove that there is room for exploring further adjustments at the carbohydrate level that could contribute to designing more efficient cancer vaccines.

    Organizational Affiliation: 

    Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química E-26006 Logroño Spain francisco.corzana@unirioja.es jesusmanuel.peregrina@unirioja.es.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ScFv_SM3A [auth H]244Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mucin-1B [auth P]6Homo sapiensMutation(s): 0 
Gene Names: MUC1, PUM
UniProt & NIH Common Fund Data Resources
Find proteins for P15941 (Homo sapiens)
Explore P15941 
Go to UniProtKB:  P15941
PHAROS:  P15941
Entity Groups  
UniProt GroupP15941
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N8W (Subject of Investigation/LOI)
Query on N8W
Download Ideal Coordinates CCD File 
G [auth P]~{N}-[(6~{S},7~{R},8~{S},8~{a}~{R})-7,8-bis(oxidanyl)-3-oxidanylidene-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyridin-6-yl]ethanamide
C9 H14 N2 O5
MKTHKMZBVDELIA-OSMVPFSASA-N		 Ligand Interaction
EDO (Subject of Investigation/LOI)
Query on EDO
Download Ideal Coordinates CCD File 
C [auth H],
D [auth H],
E [auth H],
F [auth H]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.271α = 90
b = 68.689β = 90
c = 90.393γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references