› 2ziy

X-ray diffraction
3.7Å resolution

Crystal structure of squid rhodopsin

Released:
DOI: 10.2210/pdb2ziy/pdb
PDB entry 2ziy coloured by chain, front view.
PDB entry 2ziy coloured by chain, side view.
PDB entry 2ziy coloured by chain, top view.
Source organism: Todarodes pacificus
Primary publication:
Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region.
Shimamura T, Hiraki K, Takahashi N, Hori T, Ago H, Masuda K, Takio K, Ishiguro M, Miyano M
J Biol Chem 283 17753-6 (2008)
PMID: 18463093

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-151990 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Rhodopsin Chain: A
Molecule details ›
Chain: A
Length: 372 amino acids
Theoretical weight: 41.83 KDa
Source organism: Todarodes pacificus
UniProt:
  • Canonical: P31356 (Residues: 2-373; Coverage: 83%)
Gene name: RHO
Sequence domains: 7 transmembrane receptor (rhodopsin family)
Structure domains: Rhodopsin 7-helix transmembrane proteins

Ligands and Environments

2 bound ligands:
Ligand RET 1 x RET
Ligand PLM 2 x PLM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: C2221
Unit cell:
a: 84.319Å b: 108.746Å c: 142.165Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.302 0.302 0.33

Quick links

Citations

23 review citations

Microbial and animal rhodopsins: structures, functions, and molecular mechanisms.
Ernst et al. (2014)
22 more

34 mentions without citation

Diversity and modularity of G protein-coupled receptor structures.
Katritch et al. (2012)
33 more