Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

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

Macromolecule Content

• Total Structure Weight: 50822.21 
• Atom Count: 3738 
• Residue Count: 468 
• Unique protein chains: 3

3PP4

Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for the type I / type II distinction of anti- CD20 antibodies

• DOI: 10.2210/pdb3PP4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus


• Deposited: 2010-11-24 Released: 2011-04-13 
• Deposition Author(s): Hopfner, K.-P., Lammens, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.187 
• R-Value Work: 0.137 

Literature

Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies.

Niederfellner, G., Lammens, A., Mundigl, O., Georges, G.J., Schaefer, W., Schwaiger, M., Franke, A., Wiechmann, K., Jenewein, S., Slootstra, J.W., Timmerman, P., Brannstrom, A., Lindstrom, F., Mossner, E., Umana, P., Hopfner, K.P., Klein, C.

(2011) Blood 118: 358-367

• PubMed: 21444918 
• DOI: 10.1182/blood-2010-09-305847
• Primary Citation of Related Structures:  
  3PP3


• PubMed Abstract: 
  

CD20 is a cell-surface marker of normal and malignant B cells. Rituximab, a monoclonal antibody targeting CD20, has improved the treatment of malignant lymphomas. Therapeutic CD20 antibodies are classified as either type I or II based on different mechanisms of killing malignant B cells. To reveal the molecular basis of this distinction, we fine-mapped the epitopes recognized by both types. We also determined the first X-ray structure of a type II antibody by crystallizing the obinutuzumab (GA101) Fab fragment alone and in complex with a CD20 cyclopeptide. Despite recognizing an overlapping epitope, GA101 binds CD20 in a completely different orientation than type I antibodies. Moreover, the elbow angle of GA101 is almost 30° wider than in type I antibodies, potentially resulting in different spatial arrangements of 2 CD20 molecules bound to a single GA101 or rituximab molecule. Using protein tomography, different CD20 complexes were found to be associated with the 2 antibodies, and confocal microscopy showed different membrane compartmentalization of these subpopulations of the cellular CD20 pool. Our findings offer a possible molecular explanation for the different cellular responses elicited by type I and II antibodies.

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Organizational Affiliation: 

Pharma Research and Early Development, Roche Diagnostics GmbH, Penzberg, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
GA101 Fab heavy chain	H	224	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
GA101 Fab light chain	L	219	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
B-lymphocyte antigen CD20	P	25	Homo sapiens	Mutation(s): 0  Gene Names: MS4A1 (CD20)
Find proteins for P11836 (Homo sapiens) Go to Gene View: MS4A1 Go to UniProtKB:  P11836

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	H	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.187 
• R-Value Work: 0.137 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 84.050	α = 90.00
b = 85.900	β = 116.34
c = 72.870	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
EXES	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-24 
• Released Date: 2011-04-13 
• Deposition Author(s): Hopfner, K.-P., Lammens, A.

Revision History 

• Version 1.0: 2011-04-13
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2011-07-27
  Type: Database references