6LOS image
Deposition Date 2020-01-07
Release Date 2020-09-02
Last Version Date 2023-11-29
Entry Detail
PDB ID:
6LOS
Title:
Crystal structure of mouse PEDF in complex with heterotrimeric collagen model peptide.
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.48 Å
R-Value Free:
0.28
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
C 2 2 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pigment epithelium-derived factor
Gene (Uniprot):Serpinf1
Mutagens:P374, P378, L381 deletion
Chain IDs:A
Chain Length:377
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Collagen model peptide, type I, alpha 2
Chain IDs:B (auth: F)
Chain Length:35
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Collagen model peptide, type I, alpha 1
Chain IDs:C (auth: G)
Chain Length:34
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Collagen model peptide, type I, alpha 1
Chain IDs:D (auth: H)
Chain Length:33
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Spatiotemporal regulation of PEDF signaling by type I collagen remodeling.
Proc.Natl.Acad.Sci.USA 117 11450 11458 (2020)
PMID: 32385162 DOI: 10.1073/pnas.2004034117

Abstact

Dynamic remodeling of the extracellular matrix affects many cellular processes, either directly or indirectly, through the regulation of soluble ligands; however, the mechanistic details of this process remain largely unknown. Here we propose that type I collagen remodeling regulates the receptor-binding activity of pigment epithelium-derived factor (PEDF), a widely expressed secreted glycoprotein that has multiple important biological functions in tissue and organ homeostasis. We determined the crystal structure of PEDF in complex with a disulfide cross-linked heterotrimeric collagen peptide, in which the α(I) chain segments-each containing the respective PEDF-binding region (residues 930 to 938)-are assembled with an α2α1α1 staggered configuration. The complex structure revealed that PEDF specifically interacts with a unique amphiphilic sequence, KGHRGFSGL, of the type I collagen α1 chain, with its proposed receptor-binding sites buried extensively. Molecular docking demonstrated that the PEDF-binding surface of type I collagen contains the cross-link-susceptible Lys930 residue of the α1 chain and provides a good foothold for stable docking with the α1(I) N-telopeptide of an adjacent triple helix in the fibril. Therefore, the binding surface is completely inaccessible if intermolecular crosslinking between two crosslink-susceptible lysyl residues, Lys9 in the N-telopeptide and Lys930, is present. These structural analyses demonstrate that PEDF molecules, once sequestered around newly synthesized pericellular collagen fibrils, are gradually liberated as collagen crosslinking increases, making them accessible for interaction with their target cell surface receptors in a spatiotemporally regulated manner.

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Primary Citation of related structures
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