› 4fmf

X-ray diffraction
3.2Å resolution

Crystal structure of human nectin-1 full ectodomain (D1-D3)

Released:
DOI: 10.2210/pdb4fmf/pdb
PDB entry 4fmf coloured by chain, front view.
PDB entry 4fmf coloured by chain, side view.
PDB entry 4fmf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Nectin ectodomain structures reveal a canonical adhesive interface.
Harrison OJ, Vendome J, Brasch J, Jin X, Hong S, Katsamba PS, Ahlsen G, Troyanovsky RB, Troyanovsky SM, Honig B, Shapiro L
Nat Struct Mol Biol 19 906-15 (2012)
PMID: 22902367

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172234 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Nectin-1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 313 amino acids
Theoretical weight: 35.19 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15223 (Residues: 31-337; Coverage: 63%)
Gene names: HVEC, NECTIN1, PRR1, PVRL1
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand FMT 4 x FMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P63
Unit cell:
a: 106.288Å b: 106.288Å c: 334.622Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.234 0.233 0.258
Expression system: Homo sapiens

Quick links

Citations

17 review citations

Mechanobiology of collective cell behaviours.
Ladoux et al. (2017)
16 more

6 mentions without citation

Nectin ectodomain structures reveal a canonical adhesive interface.
Harrison et al. (2012)
5 more