› 4urt

X-ray diffraction
3.1Å resolution

The crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of DCC

Released:
DOI: 10.2210/pdb4urt/pdb
PDB entry 4urt coloured by chain, front view.
PDB entry 4urt coloured by chain, side view.
PDB entry 4urt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue.
Finci LI, Krüger N, Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HDT, Svergun DI, Zhang Y, Wang JH, Meijers R
Neuron 83 839-849 (2014)
PMID: 25123307

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219145 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Netrin-1 Chain: A
Molecule details ›
Chain: A
Length: 420 amino acids
Theoretical weight: 47.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95631 (Residues: 39-453; Coverage: 72%)
Gene names: NTN1, NTN1L
Sequence domains:
Structure domains: Galactose-binding domain-like
Netrin receptor DCC Chain: B
Molecule details ›
Chain: B
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P43146 (Residues: 844-1043; Coverage: 14%)
Gene names: DCC, IGDCC1
Sequence domains: Fibronectin type III domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand CA 1 x CA
Ligand CL 1 x CL
Ligand SO4 17 x SO4
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P212121
Unit cell:
a: 84.65Å b: 87.41Å c: 155.317Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.23 0.265

Quick links

Citations

21 review citations

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

9 mentions without citation

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