Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96.24 kDa 
• Atom Count: 6727 
• Residue Count: 864 
• Unique protein chains: 3

5T78

Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide

• DOI: 10.2210/pdb5T78/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2016-09-02 Released: 2017-01-11 
• Deposition Author(s): Brooks, C.L., Movahedin, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Glycosylation of MUC1 influences the binding of a therapeutic antibody by altering the conformational equilibrium of the antigen.

Movahedin, M., Brooks, T.M., Supekar, N.T., Gokanapudi, N., Boons, G.J., Brooks, C.L.

(2017) Glycobiology 27: 677-687

• PubMed: 28025250 
• DOI: 10.1093/glycob/cww131
• Structures With Same Primary Citation


• PubMed Abstract: 
  

In cancer cells, the glycoprotein Mucin 1 (MUC1) undergoes abnormal, truncated glycosylation. The truncated glycosylation exposes cryptic peptide epitopes that can be recognized by antibodies. Since these immunogenic regions are cancer specific, they represent ideal targets for therapeutic antibodies. We investigated the role of tumor-specific glycosylation on antigen recognition by the therapeutic antibody AR20.5. We explored the affinity of AR20.5 to a synthetic cancer-specific MUC1 glycopeptide and peptide. The antibody bound to the glycopeptide with an order of magnitude stronger affinity than the naked peptide. Given these results, we postulated that AR20.5 must specifically bind the carbohydrate as well as the peptide. Using X-ray crystallography, we examined this hypothesis by determining the structure of AR20.5 in complex with both peptide and glycopeptide. Surprisingly, the structure revealed that the carbohydrate did not form any specific polar contacts with the antibody. The high affinity of AR20.5 for the glycopeptide and the lack of specific binding contacts support a hypothesis that glycosylation of MUC1 stabilizes an extended bioactive conformation of the peptide recognized by the antibody. Since high affinity binding of AR20.5 to the MUC1 glycopeptide may not driven by specific antibody-antigen contacts, but rather evidence suggests that glycosylation alters the conformational equilibrium of the antigen, which allows the antibody to select the correct conformation. This study suggests a novel mechanism of antibody-antigen interaction and also suggests that glycosylation of MUC1 is important for the generation of high affinity therapeutic antibodies.

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Organizational Affiliation: 

Department of Chemistry, California State University Fresno, 2555 E San Ramon Ave, Fresno, CA 93740, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fab fragment AR20.5 - Light Chain	A, C	216	Mus musculus	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab Fragment - AR20.5 - Heavy chain	B, D	215	Mus musculus	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
MUC1 Glycopeptide	E, F	8	Homo sapiens	Mutation(s): 0  Gene Names: MUC1, PUM
Find proteins for P15941 (Homo sapiens) Go to UniProtKB:  P15941
NIH Common Fund Data Resources
PHAROS  P15941 GTEx  ENSG00000185499

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGA	E, F	N-ACETYL-D-GALACTOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.25	α = 90
b = 100.46	β = 90
c = 235.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-02 
• Released Date: 2017-01-11 
Deposition Author(s): Brooks, C.L., Movahedin, M.

Revision History 

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-06-14
  Changes: Database references