5A2I

Crystal structure of scFv-SM3 in complex with APD-SGalNAc-RP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Deciphering the Non-Equivalence of Serine and Threonine O-Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an Anti-Muc1 Antibody.

Martinez-Saez, N.Castro-Lopez, J.Valero-Gonzalez, J.Madariaga, D.Companon, I.Somovilla, V.J.Salvado, M.Asensio, J.L.Jimenez-Barbero, J.Avenoza, A.Busto, J.H.Bernardes, G.J.L.Peregrina, J.M.Hurtado-Guerrero, R.Corzana, F.

(2015) Angew.Chem.Int.Ed.Engl. 54: 9830

  • DOI: 10.1002/anie.201502813
  • Primary Citation of Related Structures:  5A2J, 5A2K, 5A2L

  • PubMed Abstract: 
  • The structural features of MUC1-like glycopeptides bearing the Tn antigen (α-O-GalNAc-Ser/Thr) in complex with an anti MUC-1 antibody are reported at atomic resolution. For the α-O-GalNAc-Ser derivative, the glycosidic linkage adopts a high-energy co ...

    The structural features of MUC1-like glycopeptides bearing the Tn antigen (α-O-GalNAc-Ser/Thr) in complex with an anti MUC-1 antibody are reported at atomic resolution. For the α-O-GalNAc-Ser derivative, the glycosidic linkage adopts a high-energy conformation, barely populated in the free state. This unusual structure (also observed in an α-S-GalNAc-Cys mimic) is stabilized by hydrogen bonds between the peptidic fragment and the sugar. The selection of a particular peptide structure by the antibody is thus propagated to the carbohydrate through carbohydrate/peptide contacts, which force a change in the orientation of the sugar moiety. This seems to be unfeasible in the α-O-GalNAc-Thr glycopeptide owing to the more limited flexibility of the side chain imposed by the methyl group. Our data demonstrate the non-equivalence of Ser and Thr O-glycosylation points in molecular recognition processes. These features provide insight into the occurrence in nature of the APDTRP epitope for anti-MUC1 antibodies.


    Organizational Affiliation

    Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño (Spain).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IG LAMBDA-1 CHAIN V REGION S43
H
244Mus musculusN/A
Find proteins for P01801 (Mus musculus)
Go to UniProtKB:  P01801
Find proteins for P01727 (Mus musculus)
Go to UniProtKB:  P01727
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIGEN TN, SER IS COVALENTLY BOUND TO GALNAC
P
6N/AN/A
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 
P
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.181α = 90.00
b = 66.006β = 90.00
c = 90.290γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-07-08
    Type: Database references
  • Version 1.2: 2015-08-26
    Type: Database references