› 6fkn

X-ray diffraction
4.8Å resolution

Drosophila Plexin A in complex with Semaphorin 1b

Released:
DOI: 10.2210/pdb6fkn/pdb
PDB entry 6fkn coloured by chain, front view.
PDB entry 6fkn coloured by chain, side view.
PDB entry 6fkn coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Structural basis of semaphorin-plexin cis interaction.
Rozbesky D, Verhagen MG, Karia D, Nagy GN, Alvarez L, Robinson RA, Harlos K, Padilla-Parra S, Pasterkamp RJ, Jones EY
OpenAccess logo EMBO J 39 e102926 (2020)
PMID: 32500924

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-565745 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (5 distinct):
Sema domain-containing protein Chains: A, C
Molecule details ›
Chains: A, C
Length: 715 amino acids
Theoretical weight: 78.7 KDa
Source organism: Drosophila melanogaster
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9V491 (Residues: 28-730; Coverage: 37%)
Gene names: BcDNA:GM05237, CG11081, D-Plex A, DPlexA, Dmel\CG11081, Dmel_CG11081, Plex1, PlexA, PlexA1, Plexa, PlexinA, lincRNA.927, plex, plex A, plexA
Sequence domains:
Sema domain-containing protein Chains: B, D
Molecule details ›
Chains: B, D
Length: 578 amino acids
Theoretical weight: 64.21 KDa
Source organism: Drosophila melanogaster
Expression system: Homo sapiens
UniProt:
  • Canonical: Q7KK54 (Residues: 37-602; Coverage: 74%)
Gene names: BcDNA:GH03186, CG6446, D-semaIII, Dmel\CG6446, Dmel_CG6446, Sema 1b, Sema III, Sema-1b, Sema-1b-RB, Sema1b, sema-III, sema1b, semaphorin-like
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
1 bound ligand:
Ligand NAG 6 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P6522
Unit cell:
a: 153.63Å b: 153.63Å c: 425.37Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.285 0.285 0.297
Expression system: Homo sapiens

Quick links

Citations

4 review citations

Modelling and Refining Neuronal Circuits with Guidance Cues: Involvement of Semaphorins.
Limoni G. (2021)
3 more