Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.91 kDa 
• Atom Count: 3628 
• Residue Count: 435 
• Unique protein chains: 3

4TUL

Crystal structure of monoclonal antibody against neuroblastoma associated antigen.

• DOI: 10.2210/pdb4TUL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Phage #D
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2014-06-24 Released: 2015-07-15 
• Deposition Author(s): Golik, P., Grudnik, P., Dubin, G., Zdzalik, M., Rokita, H., Horwacik, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.217 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Structural Basis of GD2 Ganglioside and Mimetic Peptide Recognition by 14G2a Antibody.

Horwacik, I., Golik, P., Grudnik, P., Kolinski, M., Zdzalik, M., Rokita, H., Dubin, G.

(2015) Mol Cell Proteomics 14: 2577-2590

• PubMed: 26179345 
• DOI: 10.1074/mcp.M115.052720
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Monoclonal antibodies targeting GD2 ganglioside (GD2) have recently been approved for the treatment of high risk neuroblastoma and are extensively evaluated in clinics in other indications. This study illustrates how a therapeutic antibody distinguishes between different types of gangliosides present on normal and cancer cells and informs how synthetic peptides can imitate ganglioside in its binding to the antibody. Using high resolution crystal structures we demonstrate that the ganglioside recognition by a model antibody (14G2a) is based primarily on an extended network of direct and water molecule mediated hydrogen bonds. Comparison of the GD2-Fab structure with that of a ligand free antibody reveals an induced fit mechanism of ligand binding. These conclusions are validated by directed mutagenesis and allowed structure guided generation of antibody variant with improved affinity toward GD2. Contrary to the carbohydrate, both evaluated mimetic peptides utilize a "key and lock" interaction mechanism complementing the surface of the antibody binding groove exactly as found in the empty structure. The interaction of both peptides with the Fab relies considerably on hydrophobic contacts however, the detailed connections differ significantly between the peptides. As such, the evaluated peptide carbohydrate mimicry is defined primarily in a functional and not in structural manner.

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Organizational Affiliation: 

§Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 7 Gronostajowa St., 30-387 Krakow, Poland; ‖Malopolska Centre of Biotechnology, Jagiellonian University, 7a Gronostajowa St., 30-387 Krakow, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Heavy chain of monoclonal antibody against neuroblastoma associated antigen	H	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Light chain of monoclonal antibody against neuroblastoma associated antigen	L	220	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
peptide2	I	17	Phage #D	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	H	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.217 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.676	α = 90
b = 64.167	β = 99.46
c = 78.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-24 
• Released Date: 2015-07-15 
Deposition Author(s): Golik, P., Grudnik, P., Dubin, G., Zdzalik, M., Rokita, H., Horwacik, I.

Revision History 

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2015-07-29
  Changes: Database references
• Version 1.2: 2015-10-14
  Changes: Database references
• Version 1.3: 2018-03-07
  Changes: Data collection