› 3ol2

X-ray diffraction
2.99Å resolution

Receptor-ligand structure of Human Semaphorin 4D with Plexin B1.

Released:
DOI: 10.2210/pdb3ol2/pdb
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PDB entry 3ol2 coloured by chain, front view.
PDB entry 3ol2 coloured by chain, side view.
PDB entry 3ol2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of semaphorin-plexin signalling.
Janssen BJ, Robinson RA, Pérez-Brangulí F, Bell CH, Mitchell KJ, Siebold C, Jones EY
Nature 467 1118-22 (2010)
PMID: 20877282

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128851 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Semaphorin-4D Chain: A
Molecule details ›
Chain: A
Length: 663 amino acids
Theoretical weight: 74.32 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q92854 (Residues: 22-677; Coverage: 78%)
Gene names: C9orf164, CD100, SEMA4D, SEMAJ
Sequence domains:
Structure domains:
Plexin-B1 Chain: B
Molecule details ›
Chain: B
Length: 528 amino acids
Theoretical weight: 56.92 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43157 (Residues: 19-535; Coverage: 24%)
Gene names: KIAA0407, PLXN5, PLXNB1, SEP
Sequence domains:
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: F222
Unit cell:
a: 83.055Å b: 173.436Å c: 482.119Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.237
Expression system: Homo sapiens

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Citations

50 review citations

Semaphorins and their Signaling Mechanisms.
Alto et al. (2017)
49 more

9 mentions without citation

Plexin structures are coming: opportunities for multilevel investigations of semaphorin guidance receptors, their cell signaling mechanisms, and functions.
Hota et al. (2012)
8 more

PDB-REDO

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