9EN2 image
Deposition Date 2024-03-12
Release Date 2024-07-03
Last Version Date 2024-10-16
Entry Detail
PDB ID:
9EN2
Keywords:
Title:
Crystal structure of the metalloproteinase enhancer PCPE-1 complexed with nanobodies VHH-H4 and VHH-I5
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Lama glama (Taxon ID: 9844)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.24
R-Value Work:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Procollagen C-endopeptidase enhancer 1
Gene (Uniprot):PCOLCE
Chain IDs:A
Chain Length:302
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:VHH-H4
Chain IDs:B
Chain Length:154
Number of Molecules:1
Biological Source:Lama glama
Polymer Type:polypeptide(L)
Molecule:VHH-I5
Chain IDs:C
Chain Length:144
Number of Molecules:1
Biological Source:Lama glama
Primary Citation
Mono- and Bi-specific Nanobodies Targeting the CUB Domains of PCPE-1 Reduce the Proteolytic Processing of Fibrillar Procollagens.
J.Mol.Biol. 436 168667 168667 (2024)
PMID: 38901640 DOI: 10.1016/j.jmb.2024.168667

Abstact

The excessive deposition of fibrillar collagens is a hallmark of fibrosis. Collagen fibril formation requires proteolytic maturations by Procollagen N- and C-proteinases (PNPs and PCPs) to remove the N- and C-propeptides which maintain procollagens in the soluble form. Procollagen C-Proteinase Enhancer-1 (PCPE-1, a glycoprotein composed of two CUB domains and one NTR domain) is a regulatory protein that activates the C-terminal processing of procollagens by the main PCPs. It is often up-regulated in fibrotic diseases and represents a promising target for the development of novel anti-fibrotic strategies. Here, our objective was to develop the first antagonists of PCPE-1, based on the nanobody scaffold. Using both an in vivo selection through the immunization of a llama and an in vitro selection with a synthetic library, we generated 18 nanobodies directed against the CUB domains of PCPE1, which carry its enhancing activity. Among them, I5 from the immune library and H4 from the synthetic library have a high affinity for PCPE-1 and inhibit its interaction with procollagens. The crystal structure of the complex formed by PCPE-1, H4 and I5 showed that they have distinct epitopes and enabled the design of a biparatopic fusion, the diabody diab-D1. Diab-D1 has a sub-nanomolar affinity for PCPE-1 and is a potent antagonist of its activity, preventing the stimulation of procollagen cleavage in vitro. Moreover, Diab-D1 is also effective in reducing the proteolytic maturation of procollagen I in cultures of human dermal fibroblasts and hence holds great promise as a tool to modulate collagen deposition in fibrotic conditions.

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