Crystal structure of rhombohedral crystal form of ground-state rhodopsin

Experimental Data Snapshot

  • Resolution: 3.80 Å
  • R-Value Free: 0.418 
  • R-Value Work: 0.373 
  • R-Value Observed: 0.375 

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Crystal structure of a photoactivated deprotonated intermediate of rhodopsin.

Salom, D.Lodowski, D.T.Stenkamp, R.E.Trong, I.L.Golczak, M.Jastrzebska, B.Harris, T.Ballesteros, J.A.Palczewski, K.

(2006) Proc Natl Acad Sci U S A 103: 16123-16128

  • DOI: https://doi.org/10.1073/pnas.0608022103
  • Primary Citation of Related Structures:  
    2I35, 2I36, 2I37

  • PubMed Abstract: 

    The changes that lead to activation of G protein-coupled receptors have not been elucidated at the structural level. In this work we report the crystal structures of both ground state and a photoactivated deprotonated intermediate of bovine rhodopsin at a resolution of 4.15 A. In the photoactivated state, the Schiff base linking the chromophore and Lys-296 becomes deprotonated, reminiscent of the G protein-activating state, metarhodopsin II. The structures reveal that the changes that accompany photoactivation are smaller than previously predicted for the metarhodopsin II state and include changes on the cytoplasmic surface of rhodopsin that possibly enable the coupling to its cognate G protein, transducin. Furthermore, rhodopsin forms a potentially physiologically relevant dimer interface that involves helices I, II, and 8, and when taken with the prior work that implicates helices IV and V as the physiological dimer interface may account for one of the interfaces of the oligomeric structure of rhodopsin seen in the membrane by atomic force microscopy. The activation and oligomerization models likely extend to the majority of other G protein-coupled receptors.

  • Organizational Affiliation

    Novasite Pharmaceuticals Inc., San Diego, CA 92121, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhodopsin349Bos taurusMutation(s): 0 
Membrane Entity: Yes 
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02699
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Resolution: 3.80 Å
  • R-Value Free: 0.418 
  • R-Value Work: 0.373 
  • R-Value Observed: 0.375 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 277.534α = 90
b = 277.534β = 90
c = 66.321γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary