8OL9 image
Entry Detail
PDB ID:
8OL9
Keywords:
Title:
Anti-FIXa Fab in complex with human des-(Gla-EGF1) FIXa
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-03-30
Release Date:
2023-07-19
Method Details:
Experimental Method:
Resolution:
2.60 Å
R-Value Free:
0.32
R-Value Work:
0.26
R-Value Observed:
0.26
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Light chain of FIXa binding Fab
Chain IDs:A
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Heavy chain of FIXa binding Fab
Chain IDs:B
Chain Length:225
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Coagulation factor IX heavy chain
Chain IDs:C (auth: H)
Chain Length:235
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Coagulation factor IX light chain
Chain IDs:D (auth: L)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Computational design of N-linked glycans for high throughput epitope profiling.
Protein Sci. 32 e4726 e4726 (2023)
PMID: 37421602 DOI: 10.1002/pro.4726

Abstact

Efficient identification of epitopes is crucial for drug discovery and design as it enables the selection of optimal epitopes, expansion of lead antibody diversity, and verification of binding interface. Although high-resolution low throughput methods like x-ray crystallography can determine epitopes or protein-protein interactions accurately, they are time-consuming and can only be applied to a limited number of complexes. To overcome these limitations, we have developed a rapid computational method that incorporates N-linked glycans to mask epitopes or protein interaction surfaces, thereby providing a mapping of these regions. Using human coagulation factor IXa (fIXa) as a model system, we computationally screened 158 positions and expressed 98 variants to test experimentally for epitope mapping. We were able to delineate epitopes rapidly and reliably through the insertion of N-linked glycans that efficiently disrupted binding in a site-selective manner. To validate the efficacy of our method, we conducted ELISA experiments and high-throughput yeast surface display assays. Furthermore, x-ray crystallography was employed to verify the results, thereby recapitulating through the method of N-linked glycans a coarse-grained mapping of the epitope.

Legend

Protein

Chemical

Disease

Primary Citation of related structures