› 4gz8

X-ray diffraction
3.3Å resolution

Mouse Semaphorin 3A, domains Sema-PSI-IG

Released:
DOI: 10.2210/pdb4gz8/pdb
PDB entry 4gz8 coloured by chain, front view.
PDB entry 4gz8 coloured by chain, side view.
PDB entry 4gz8 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex.
Janssen BJ, Malinauskas T, Weir GA, Cader MZ, Siebold C, Jones EY
Nat Struct Mol Biol 19 1293-9 (2012)
PMID: 23104057

Function and Biology Details

Biochemical function:
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-126647 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Semaphorin-3A Chains: A, B
Molecule details ›
Chains: A, B
Length: 667 amino acids
Theoretical weight: 72.42 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: O08665 (Residues: 21-569; Coverage: 73%)
Gene names: SemD, Sema3a, Semad
Sequence domains: Sema domain
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand CA 5 x CA
Ligand ACT 2 x ACT
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 97.63Å b: 126.17Å c: 161.48Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.213 0.265
Expression system: Homo sapiens

Quick links

Citations

39 review citations

Semaphorins and plexins as therapeutic targets.
Worzfeld et al. (2014)
38 more

6 mentions without citation

Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex.
Janssen et al. (2012)
5 more