› 4jhp

X-ray diffraction
1.9Å resolution

The crystal structure of the RPGR RCC1-like domain in complex with PDE6D

Released:
DOI: 10.2210/pdb4jhp/pdb
PDB entry 4jhp coloured by chain, front view.
PDB entry 4jhp coloured by chain, side view.
PDB entry 4jhp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo.
Wätzlich D, Vetter I, Gotthardt K, Miertzschke M, Chen YX, Wittinghofer A, Ismail S
EMBO Rep 14 465-72 (2013)
PMID: 23559067

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-129179 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta Chain: B
Molecule details ›
Chain: B
Length: 152 amino acids
Theoretical weight: 17.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43924 (Residues: 1-150; Coverage: 100%)
Gene names: PDE6D, PDED
Sequence domains: GMP-PDE, delta subunit
Structure domains: GMP phosphodiesterase, delta subunit
X-linked retinitis pigmentosa GTPase regulator Chain: C
Molecule details ›
Chain: C
Length: 391 amino acids
Theoretical weight: 42.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q92834 (Residues: 7-368; Coverage: 36%)
Gene names: RP3, RPGR, XLRP3
Sequence domains: Regulator of chromosome condensation (RCC1) repeat
Structure domains: Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2
Unit cell:
a: 133.83Å b: 58.78Å c: 92.11Å
α: 90° β: 123.32° γ: 90°
R-values:
R R work R free
0.201 0.2 0.221
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Open Sesame: How Transition Fibers and the Transition Zone Control Ciliary Composition.
Garcia-Gonzalo et al. (2017)
10 more

4 mentions without citation

The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo.
Wätzlich et al. (2013)
3 more