9DVQ

Cryo-EM structure of Human Fibroblast Activation Protein alpha dimer with one SUMO-I3 VHHs bound

Summary for 9DVQ

• Entry DOI: 10.2210/pdb9dvq/pdb
• EMDB information: 47215
• Descriptor: Antiplasmin-cleaving enzyme FAP, soluble form, SUMO-I3, 2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
• Functional Keywords: fibroblast activation protein, single domain antibody, protease, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 201240.40

Authors

Xu, Z.,Schnicker, N.J.,Wadas, T.J. (deposition date: 2024-10-08, release date: 2025-02-26, Last modification date: 2025-03-05)

Primary citation

Xu, Z.,Sinha, A.,Pandya, D.N.,Schnicker, N.J.,Wadas, T.J.
Cryo-electron microscopy reveals a single domain antibody with a unique binding epitope on fibroblast activation protein alpha.
Rsc Chem Biol, 2025

PubMed Abstract: Fibroblast activation protein alpha (FAP) is a serine protease that is expressed at basal levels in benign tissues but is overexpressed in a variety of pathologies, including cancer. Despite this unique expression profile, designing functional diagnostic and therapeutic agents that effectively target this biomarker remains elusive. Here we report the structural characterization of the interaction between a novel single domain antibody (sdAb), I3, and FAP using cryo-electron microscopy. The reconstructions were determined to a resolution of 2.7 Å and contained two distinct populations; one I3 bound and two I3 molecules bound to the FAP dimer. In both cases, the sdAb bound a unique epitope that was distinct from the active site of the enzyme. Furthermore, this report describes the rational mutation of specific residues within the complementarity determining region 3 (CDR3) loop to enhance affinity and selectivity of the I3 molecule for FAP. This report represents the first sdAb-FAP structure to be described in the literature.

PubMed: 39975582
DOI: 10.1039/d4cb00267a

Experimental method

ELECTRON MICROSCOPY (2.7 Å)