Crystal structure of squid rhodopsin

Experimental Data Snapshot

  • Resolution: 3.70 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.302 

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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.

(2008) J Biol Chem 283: 17753-17756

  • DOI: https://doi.org/10.1074/jbc.C800040200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    G-protein-coupled receptors play a key step in cellular signal transduction cascades by transducing various extracellular signals via G-proteins. Rhodopsin is a prototypical G-protein-coupled receptor involved in the retinal visual signaling cascade. We determined the structure of squid rhodopsin at 3.7A resolution, which transduces signals through the G(q) protein to the phosphoinositol cascade. The structure showed seven transmembrane helices and an amphipathic helix H8 has similar geometry to structures from bovine rhodopsin, coupling to G(t), and human beta(2)-adrenergic receptor, coupling to G(s). Notably, squid rhodopsin contains a well structured cytoplasmic region involved in the interaction with G-proteins, and this region is flexible or disordered in bovine rhodopsin and human beta(2)-adrenergic receptor. The transmembrane helices 5 and 6 are longer and extrude into the cytoplasm. The distal C-terminal tail contains a short hydrophilic alpha-helix CH after the palmitoylated cysteine residues. The residues in the distal C-terminal tail interact with the neighboring residues in the second cytoplasmic loop, the extruded transmembrane helices 5 and 6, and the short helix H8. Additionally, the Tyr-111, Asn-87, and Asn-185 residues are located within hydrogen-bonding distances from the nitrogen atom of the Schiff base.

  • Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, Kouto, Sayo, Hyogo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhodopsin372Todarodes pacificusMutation(s): 0 
Membrane Entity: Yes 
Find proteins for P31356 (Todarodes pacificus)
Explore P31356 
Go to UniProtKB:  P31356
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31356
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.70 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.302 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.319α = 90
b = 108.746β = 90
c = 142.165γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description