7NDG image
Deposition Date 2021-02-01
Release Date 2021-03-31
Last Version Date 2024-11-06
Entry Detail
PDB ID:
7NDG
Title:
Cryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive Guidance Molecule B
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Mus musculus (Taxon ID: 10090)
Host Organism:
Method Details:
Experimental Method:
Resolution:
5.98 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Netrin-1
Gene (Uniprot):NTN1
Chain IDs:A, F (auth: G), I (auth: D)
Chain Length:441
Number of Molecules:3
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Neogenin
Gene (Uniprot):Neo1
Chain IDs:B, G (auth: H), J (auth: E)
Chain Length:354
Number of Molecules:3
Biological Source:Mus musculus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Repulsive Guidance Molecule B (C-terminal region)
Gene (Uniprot):RGMB
Chain IDs:C (auth: F), E (auth: C), K (auth: I)
Chain Length:252
Number of Molecules:3
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RGM domain family member B
Gene (Uniprot):RGMB
Chain IDs:D (auth: N), H (auth: M), L (auth: O)
Chain Length:119
Number of Molecules:3
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