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 3TJE | pdb_00003tje

Crystal structure of Fas receptor extracellular domain in complex with Fab E09


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.232 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3TJE

This is version 1.4 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1038/cdd.2011.208
  • Primary Citation 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.


  • Organizational Affiliation: 
    • MedImmune Ltd., Granta Park, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 67.22 kDa 
  • Atom Count: 4,573 
  • Modeled Residue Count: 542 
  • Deposited Residue Count: 617 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab E09, light chainA [auth L]216Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab E09, heavy chainB [auth H]245Homo sapiensMutation(s): 0 
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 6C [auth F]156Homo sapiensMutation(s): 0 
Gene Names: APT1, FAS, FAS1, TNFRSF6
UniProt & NIH Common Fund Data Resources
Find proteins for P25445 (Homo sapiens)
Explore P25445 
Go to UniProtKB:  P25445
PHAROS:  P25445
GTEx:  ENSG00000026103 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25445
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD

Query on CD



Download:Ideal Coordinates CCD File
J [auth F],
K [auth F]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth L],
E [auth L],
F [auth L],
G [auth L],
I [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth L]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.232 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.49α = 90
b = 166.4β = 90
c = 110.72γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary