Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 67.71 kDa 
• Atom Count: 4325 
• Residue Count: 519 
• Unique protein chains: 3

3THM

Crystal structure of Fas receptor extracellular domain in complex with Fab EP6b_B01

• DOI: 10.2210/pdb3THM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-19 Released: 2012-05-09 
• Deposition Author(s): Zuger, S., Stirnimann, C., Briand, C., Grutter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.221 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

A series of Fas receptor agonist antibodies that demonstrate an inverse correlation between affinity and potency.

Chodorge, M., Zuger, S., Stirnimann, C., Briand, C., Jermutus, L., Grutter, M.G., Minter, R.R.

(2012) Cell Death Differ 19: 1187-1195

• PubMed: 22261618 
• DOI: 10.1038/cdd.2011.208
• Primary Citation of Related Structures:  
  3THM, 3TJE


• PubMed Abstract: 
  

Receptor agonism remains poorly understood at the molecular and mechanistic level. In this study, we identified a fully human anti-Fas antibody that could efficiently trigger apoptosis and therefore function as a potent agonist. Protein engineering and crystallography were used to mechanistically understand the agonistic activity of the antibody. The crystal structure of the complex was determined at 1.9 Å resolution and provided insights into epitope recognition and comparisons with the natural ligand FasL (Fas ligand). When we affinity-matured the agonist antibody, we observed that, surprisingly, the higher-affinity antibodies demonstrated a significant reduction, rather than an increase, in agonist activity at the Fas receptor. We propose and experimentally demonstrate a model to explain this non-intuitive impact of affinity on agonist antibody signalling and explore the implications for the discovery of therapeutic agonists in general.

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Organizational Affiliation: 

MedImmune Ltd., Granta Park, Cambridge, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab EP6b_B01, light chain	L	216	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab EP6b_B01, heavy chain	H	245	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 6	F	156	Homo sapiens	Mutation(s): 0  Gene Names: APT1, FAS, FAS1, TNFRSF6
Find proteins for P25445 (Homo sapiens) Explore P25445  Go to UniProtKB:  P25445
NIH Common Fund Data Resources
PHAROS  P25445 GTEx  ENSG00000026103

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	A	3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	L	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.221 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.51	α = 90
b = 94.51	β = 90
c = 139.2	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-19 
• Released Date: 2012-05-09 
Deposition Author(s): Zuger, S., Stirnimann, C., Briand, C., Grutter, M.G.

Revision History 

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2012-06-27
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary