› 4plo

X-ray diffraction
2.9Å resolution

Crystal Structure of chicken Netrin-1 (LN-LE3) in complex with mouse DCC (FN4-5)

Released:
DOI: 10.2210/pdb4plo/pdb
PDB entry 4plo coloured by chain, front view.
PDB entry 4plo coloured by chain, side view.
PDB entry 4plo coloured by chain, top view.
Source organisms:
Primary publication:
Neural migration. Structures of netrin-1 bound to two receptors provide insight into its axon guidance mechanism.
Xu K, Wu Z, Renier N, Antipenko A, Tzvetkova-Robev D, Xu Y, Minchenko M, Nardi-Dei V, Rajashankar KR, Himanen J, Tessier-Lavigne M, Nikolov DB
Science 344 1275-9 (2014)
PMID: 24876346

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159718 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Netrin receptor DCC Chain: B
Molecule details ›
Chain: B
Length: 206 amino acids
Theoretical weight: 22.77 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: P70211 (Residues: 721-942; Coverage: 14%)
Gene name: Dcc
Sequence domains: Fibronectin type III domain
Structure domains: Immunoglobulins
Netrin-1 Chain: A
Molecule details ›
Chain: A
Length: 432 amino acids
Theoretical weight: 48.55 KDa
Source organism: Gallus gallus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q90922 (Residues: 26-457; Coverage: 74%)
Gene name: NTN1
Sequence domains:
Structure domains: Galactose-binding domain-like

Ligands and Environments

3 bound ligands:
Ligand NAG 3 x NAG
Ligand SO4 5 x SO4
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 49.478Å b: 72.939Å c: 285.159Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.224 0.288
Expression system: Homo sapiens

Quick links

Citations

30 review citations

Revisiting Netrin-1: One Who Guides (Axons).
Boyer et al. (2018)
29 more

6 mentions without citation

DCC mutation update: Congenital mirror movements, isolated agenesis of the corpus callosum, and developmental split brain syndrome.
Marsh et al. (2018)
5 more