› 5f2u

X-ray diffraction
1.85Å resolution

Structure of Fully modified farnesylated INPP5E Peptide in complex with PDE6D

Released:
DOI: 10.2210/pdb5f2u/pdb
PDB entry 5f2u coloured by chain, front view.
PDB entry 5f2u coloured by chain, side view.
PDB entry 5f2u coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
PDE6δ-mediated sorting of INPP5E into the cilium is determined by cargo-carrier affinity.
Fansa EK, Kösling SK, Zent E, Wittinghofer A, Ismail S
Nat Commun 7 11366 (2016)
PMID: 27063844

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129175 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta Chains: A, B
Molecule details ›
Chains: A, B
Length: 149 amino acids
Theoretical weight: 17.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43924 (Residues: 2-150; Coverage: 99%)
Gene names: PDE6D, PDED
Sequence domains: GMP-PDE, delta subunit
Structure domains: GMP phosphodiesterase, delta subunit
Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, s-farnesyl-l-cysteine methyl ester Chains: C, D
Molecule details ›
Chains: C, D
Length: 5 amino acids
Theoretical weight: 524 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand FAR 2 x FAR
1 modified residue:
Ligand CMT 2 x CMT

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2221
Unit cell:
a: 77.47Å b: 81.2Å c: 117.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.208
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

16 review citations

Establishing and regulating the composition of cilia for signal transduction.
Nachury et al. (2019)
15 more

7 mentions without citation

Sorting of lipidated cargo by the Arl2/Arl3 system.
Fansa et al. (2016)
6 more