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

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab EP6b_B01, light chainA [auth L]216Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab EP6b_B01, heavy chainB [auth H]245Homo sapiensMutation(s): 0 
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: APT1FASFAS1TNFRSF6
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