3SKJ | pdb_00003skj

Structural And Functional Characterization of an Agonistic Anti-Human EphA2 Monoclonal Antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.271 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural and functional characterization of an agonistic anti-human EphA2 monoclonal antibody.

Peng, L.Oganesyan, V.Damschroder, M.M.Wu, H.Dall'Acqua, W.F.

(2011) J Mol Biology 413: 390-405

  • DOI: https://doi.org/10.1016/j.jmb.2011.08.018
  • Primary Citation Related Structures: 
    3SKJ

  • PubMed Abstract: 

    We report here the three-dimensional structure of human ephrin type A receptor 2 (EphA2) bound to the Fab (fragment antigen binding) of an agonistic human antibody (1C1; IgG1/κ). The structure of the corresponding complex was solved at a resolution of 2.5 Å using molecular replacement and constitutes the first reported structure of a human ephrin receptor bound to an antibody. We have also defined the corresponding functional epitope using a mutagenesis-based approach. This study revealed discrete structural features that determine the fine specificity of 1C1 to EphA2. Our data also provided a molecular basis for 1C1 mechanism of action. More precisely, we propose that its agonistic, internalizing properties are the result of ligand mimicry by the third heavy-chain complementarity-determining region of 1C1. Because EphA2 is an important contributor to cancer formation and progression, these findings may have implications for designing the next generation of anti-tumor therapies.


  • Organizational Affiliation
    • Department of Antibody Discovery and Protein Engineering, MedImmune, Gaithersburg, MD 20878, USA.

Macromolecule Content 

  • Total Structure Weight: 142.94 kDa 
  • Atom Count: 8,819 
  • Modeled Residue Count: 1,144 
  • Deposited Residue Count: 1,302 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody, light chainA [auth L],
C [auth M]
214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody, heavy chainB [auth H],
D [auth I]
231Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Ephrin type-A receptor 2
E, F
206Homo sapiensMutation(s): 0 
Gene Names: EPHA2ECK
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens)
Explore P29317 
Go to UniProtKB:  P29317
PHAROS:  P29317
GTEx:  ENSG00000142627 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29317
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.271 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.94α = 90
b = 120.859β = 90
c = 286.238γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-09-07
    Changes: Database references
  • Version 1.2: 2012-08-29
    Changes: Database references
  • Version 1.3: 2017-05-31
    Changes: Structure summary
  • Version 1.4: 2024-11-27
    Changes: Data collection, Database references, Structure summary