7NE0 image
Deposition Date 2021-02-02
Release Date 2021-03-31
Last Version Date 2024-11-06
Entry Detail
PDB ID:
7NE0
Title:
Structure of the ternary complex between Netrin-1, Repulsive-Guidance Molecule-B (RGMB) and Neogenin
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Mus musculus (Taxon ID: 10090)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.25 Å
R-Value Free:
0.26
R-Value Work:
0.24
R-Value Observed:
0.25
Space Group:
H 3 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Netrin-1
Gene (Uniprot):NTN1
Chain IDs:A
Chain Length:444
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Neogenin
Gene (Uniprot):Neo1
Chain IDs:B
Chain Length:354
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Repulsive Guidance Molecule B
Gene (Uniprot):RGMB
Chain IDs:C
Chain Length:35
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Repulsive Guidance Molecule B C-terminal region (chain D)
Gene (Uniprot):RGMB
Chain IDs:D
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation

Abstact

During cell migration or differentiation, cell surface receptors are simultaneously exposed to different ligands. However, it is often unclear how these extracellular signals are integrated. Neogenin (NEO1) acts as an attractive guidance receptor when the Netrin-1 (NET1) ligand binds, but it mediates repulsion via repulsive guidance molecule (RGM) ligands. Here, we show that signal integration occurs through the formation of a ternary NEO1-NET1-RGM complex, which triggers reciprocal silencing of downstream signaling. Our NEO1-NET1-RGM structures reveal a "trimer-of-trimers" super-assembly, which exists in the cell membrane. Super-assembly formation results in inhibition of RGMA-NEO1-mediated growth cone collapse and RGMA- or NET1-NEO1-mediated neuron migration, by preventing formation of signaling-compatible RGM-NEO1 complexes and NET1-induced NEO1 ectodomain clustering. These results illustrate how simultaneous binding of ligands with opposing functions, to a single receptor, does not lead to competition for binding, but to formation of a super-complex that diminishes their functional outputs.

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Primary Citation of related structures