Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.87 kDa 
• Atom Count: 2727 
• Residue Count: 330 
• Unique protein chains: 1

2I35

Crystal structure of rhombohedral crystal form of ground-state rhodopsin

• DOI: 10.2210/pdb2I35/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2006-08-17 Released: 2006-10-17 
• Deposition Author(s): Stenkamp, R.E., Le Trong, I., Lodowski, D.T., Salom, D., Palczewski, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.418 
• R-Value Work: 0.373 
• R-Value Observed: 0.375 

Literature

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

• PubMed: 17060607 
• DOI: 10.1073/pnas.0608022103
• Primary Citation of Related Structures:  
  2I37, 2I36, 2I35


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A	349	Bos taurus	Mutation(s): 0  Gene Names: RHO
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors: Class A	Protein:  Rhodopsin, photoactivated
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	A	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
PLM	A	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 277.534	α = 90
b = 277.534	β = 90
c = 66.321	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-17 
• Released Date: 2006-10-17 
Deposition Author(s): Stenkamp, R.E., Le Trong, I., Lodowski, D.T., Salom, D., Palczewski, K.

Revision History 

• 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