› 4ww3

X-ray diffraction
2.8Å resolution

Crystal structure of the lumi intermediate of squid rhodopsin

Released:
DOI: 10.2210/pdb4ww3/pdb
PDB entry 4ww3 coloured by chain, front view.
PDB entry 4ww3 coloured by chain, side view.
PDB entry 4ww3 coloured by chain, top view.
Source organism: Todarodes pacificus
Primary publication:
Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin.
Murakami M, Kouyama T
OpenAccess logo PLoS One 10 e0126970 (2015)
PMID: 26024518

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151990 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Rhodopsin Chains: A, B
Molecule details ›
Chains: A, B
Length: 350 amino acids
Theoretical weight: 39.52 KDa
Source organism: Todarodes pacificus
UniProt:
  • Canonical: P31356 (Residues: 9-358; Coverage: 78%)
Gene name: RHO
Sequence domains: 7 transmembrane receptor (rhodopsin family)
Structure domains: Rhodopsin 7-helix transmembrane proteins

Ligands and Environments

6 bound ligands:
Ligand RET 2 x RET
Ligand PLM 4 x PLM
Ligand TWT 2 x TWT
Ligand BOG 2 x BOG
Ligand SO4 1 x SO4
Ligand PC1 1 x PC1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P62
Unit cell:
a: 122.39Å b: 122.39Å c: 158.77Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.29 0.29 0.296

Quick links

Citations

1 review citation

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering.
de Grip et al. (2022)
5 other articles

3 mentions without citation

G Protein-Coupled Receptors Contain Two Conserved Packing Clusters.
Sanchez-Reyes et al. (2017)
2 more