Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26992.66 
• Atom Count: 1802 
• Residue Count: 250 
• Unique protein chains: 2

5A2K

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

• DOI: 10.2210/pdb5A2K/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Komagataella pastoris


• Deposited: 2015-05-20 Released: 2015-06-03 
• Deposition Author(s): 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.

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Experimental Data Snapshot

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

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

• PubMed: 26118689 
• DOI: 10.1002/anie.201502813
• Primary Citation of Related Structures:  
  5A2L, 5A2J, 5A2I


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
IG LAMBDA-1 CHAIN V REGION S43	H	244	Mus musculus	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
ANTIGEN TN, THR IS COVALENTLY BOUND TO GALNAC	P	6	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	H	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
A2G	P	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N

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 = 35.418	α = 90.00
b = 68.796	β = 90.00
c = 90.414	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-05-20 
• Released Date: 2015-06-03 
• Deposition Author(s): 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.

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