› 7ndg

Electron Microscopy
5.98Å resolution

Cryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive Guidance Molecule B

Released:
DOI: 10.2210/pdb7ndg/pdb
PDB entry 7ndg coloured by chain, front view.
PDB entry 7ndg coloured by chain, side view.
PDB entry 7ndg coloured by chain, top view.
Source organisms:
Primary publication:
Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling.
Robinson RA, Griffiths SC, van de Haar LL, Malinauskas T, van Battum EY, Zelina P, Schwab RA, Karia D, Malinauskaite L, Brignani S, van den Munkhof MH, Düdükcü Ö, De Ruiter AA, Van den Heuvel DMA, Bishop B, Elegheert J, Aricescu AR, Pasterkamp RJ, Siebold C
OpenAccess logo Cell 184 2103-2120.e31 (2021)
PMID: 33740419
Related structures: EMD-12286

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-131964 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Netrin-1 Chains: A, D, G
Molecule details ›
Chains: A, D, G
Length: 441 amino acids
Theoretical weight: 49.23 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O95631 (Residues: 25-453; Coverage: 74%)
Gene names: NTN1, NTN1L
Sequence domains:
Neogenin Chains: B, E, H
Molecule details ›
Chains: B, E, H
Length: 354 amino acids
Theoretical weight: 39.27 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q7TQG5 (Residues: 766-1107; Coverage: 24%)
Gene name: Neo1
Sequence domains: Fibronectin type III domain
Repulsive guidance molecule B Chains: C, F, I
Repulsive guidance molecule B Chains: M, N, O

Ligands and Environments

2 bound ligands:
Ligand CA 3 x CA
Ligand NAG 12 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 5.98Å
Relevant EMDB volumes: EMD-12286
Expression system: Homo sapiens

Quick links

Citations

8 review citations

Unraveling Axon Guidance during Axotomy and Regeneration.
Domínguez-Romero et al. (2021)
7 more

1 mention without citation

Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling.
Robinson et al. (2021)