› 6fkm

X-ray diffraction
2.96Å resolution

Drosophila Plexin A in complex with Semaphorin 1b

Released:
DOI: 10.2210/pdb6fkm/pdb
Model geometry
Fit model/data
PDB entry 6fkm coloured by chain, front view.
PDB entry 6fkm coloured by chain, side view.
PDB entry 6fkm 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-181588 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Sema domain-containing protein Chain: A
Molecule details ›
Chain: A
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 Chain: B
Molecule details ›
Chain: B
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:
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
1 bound ligand:
Ligand NAG 4 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: C2221
Unit cell:
a: 130.94Å b: 195.09Å c: 124.84Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.186 0.246
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