5A2K

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 

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:  

  • 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

    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK).,Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Edificio I+D, 50018 Zaragoza (Spain).,Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño (Spain). jesusmanuel.peregrina@unirioja.es.,Instituto de Química Orgánica General, IQOG-CSIC, Juan de la Cierva 3, 28006 Madrid (Spain).,Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain).,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao (Spain).,Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa (Portugal).,Fundación ARAID, Edificio Pignatelli 36, Zaragoza (Spain).,Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia Building 801 A, 48160 Derio (Spain).,Fundación ARAID, Edificio Pignatelli 36, Zaragoza (Spain). rhurtado@bifi.es.,Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, C/Marcellí Domingo s/n, 43007 Tarragona (Spain).,Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Edificio I+D, 50018 Zaragoza (Spain). rhurtado@bifi.es.,Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño (Spain). francisco.corzana@unirioja.es.,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 musculusMutation(s): 0 
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, THR IS COVALENTLY BOUND TO GALNAC
P
6N/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 
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: 1.7 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.418α = 90.00
b = 68.796β = 90.00
c = 90.414γ = 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