7VG7 image
Deposition Date 2021-09-14
Release Date 2022-08-17
Last Version Date 2024-11-13
Entry Detail
PDB ID:
7VG7
Title:
Plexin B1 extracellular fragment in complex with lasso-grafted PB1m6A9 peptide
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.24
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Plexin-B1
Gene (Uniprot):PLXNB1
Mutagens:T19S
Chain IDs:A
Chain Length:525
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uteroglobin,PB1m6A9 peptide,Uteroglobin
Gene (Uniprot):SCGB1A1
Mutagens:A21S
Chain IDs:B
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function.
Structure 30 1411 1423.e4 (2022)
PMID: 35981535 DOI: 10.1016/j.str.2022.07.008

Abstact

Signaling by single-pass transmembrane receptors often involves a formation of ligand-induced receptor dimers with particular conformation, and bivalent receptor binders can modulate receptor functions by inducing different receptor dimer conformations, although such agents are difficult to design. Here, we describe the generation of both antagonistic and agonistic receptor dimerizers toward PlexinB1 (PlxnB1), a receptor for semaphorin 4D (Sema4D), by grafting two different PlxnB1-binding peptides onto the human immunoglobulin G1 (IgG1) Fc protein. The function-modulating activity of a peptide Fc was strongly dependent on the type of the peptide as well as the grafting site, with the best variants showing activity at an nM concentration range. Structural analysis of each peptide-PlxnB1 complex revealed that the agonistic Fc dimerizes PlxnB1 in a face-to-face fashion similar to that induced by Sema4D, whereas antagonistic Fc would induce signaling-incompetent PlxnB1 dimer conformation, enforcing the idea that plexin activation is primarily controlled by the receptor orientation within the dimer.

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