8T9B image
Deposition Date 2023-06-23
Release Date 2024-05-01
Last Version Date 2025-06-04
Entry Detail
PDB ID:
8T9B
Keywords:
Title:
Structure of the CK variant of Fab F1 (FabC-F1) in complex with the C-terminal FN3 domain of EphA2
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
4.20 Å
R-Value Free:
0.31
R-Value Work:
0.29
R-Value Observed:
0.29
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:CK variant of Fab F1 heavy chain
Chain IDs:A (auth: C), C (auth: A), E (auth: D), G (auth: F)
Chain Length:237
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:CK variant of Fab F1 light chain
Mutations:HAGLSSP replaced by QGTTS
Chain IDs:B (auth: G), D (auth: B), F (auth: E), H
Chain Length:214
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Ephrin type-A receptor 2
Gene (Uniprot):EPHA2
Chain IDs:I, J, K, L
Chain Length:98
Number of Molecules:4
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Synthetic antibodies targeting EphA2 induce diverse signaling-competent clusters with differential activation.
Protein Sci. 34 e70145 e70145 (2025)
PMID: 40411427 DOI: 10.1002/pro.70145

Abstact

The receptor tyrosine kinase EphA2 interacts with ephrin (Efn) ligands to mediate bi-directional signals that drive cellular sorting processes during tissue development. In the context of various cancers, EphA2 can also drive invasive metastatic disease and represents an important target for cancer therapeutics. Natural Efn ligands sterically seed intertwined EphA2 clusters capable of recruiting intracellular kinases to mediate trans-phosphorylation. Synthetic proteins, such as antibodies (Abs), can mimic Efn ligands to trigger EphA2 signaling, leading to receptor internalization and degradation, and enabling intracellular delivery of conjugated drugs. Furthermore, Abs are capable of recruiting EphA2 into clusters distinct from those seeded by Efn. We developed three synthetic Abs targeting distinct EphA2 domains and determined the paratope valency necessary for agonist or antagonist properties of each of the three epitopes. Structural modeling of monovalent Fabs in complex with EphA2 elucidated competitive and non-competitive mechanisms of inhibition of EphA2 canonical signaling. Likewise, modeling of clusters induced by bivalent IgGs elucidated multiple signaling-competent EphA2 clusters capable of triggering a continuum of signaling strengths and provided insights into the requirement for multimerization of EphA2 to trigger phosphorylation. Our study shows how different agonist clusters lead to distinct kinase recruitment efficiencies to modify phosphotyrosine signal strength, and provides a panel of anti-EphA2 Abs as reagents for the development of therapeutics.

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Primary Citation of related structures