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 3THM | pdb_00003thm

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.221 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.183 (Depositor) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 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: 67.71 kDa 
  • Atom Count: 4,325 
  • Modeled Residue Count: 519 
  • Deposited Residue Count: 617 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab EP6b_B01, light chainA [auth L]216Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab EP6b_B01, heavy chainB [auth H]245Homo sapiensMutation(s): 0 
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Reference Sequence
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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
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.221 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.183 (Depositor) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.51α = 90
b = 94.51β = 90
c = 139.2γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary