Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82820.27 
• Atom Count: 5494 
• Residue Count: 696 
• Unique protein chains: 1

3CAP

Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State

• DOI: 10.2210/pdb3CAP/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus


• Deposited: 2008-02-20 Released: 2008-06-24 
• Deposition Author(s): Park, J.H., Scheerer, P., Hofmann, K.P., Choe, H.-W., Ernst, O.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.266 
• R-Value Work: 0.229 

Literature

Crystal structure of the ligand-free G-protein-coupled receptor opsin

Park, J.H., Scheerer, P., Hofmann, K.P., Choe, H.-W., Ernst, O.P.

(2008) Nature 454: 183-187

• PubMed: 18563085 
• DOI: 10.1038/nature07063


• PubMed Abstract: 
  

In the G-protein-coupled receptor (GPCR) rhodopsin, the inactivating ligand 11-cis-retinal is bound in the seven-transmembrane helix (TM) bundle and is cis/trans isomerized by light to form active metarhodopsin II. With metarhodopsin II decay, all-trans-retinal is released, and opsin is reloaded with new 11-cis-retinal. Here we present the crystal structure of ligand-free native opsin from bovine retinal rod cells at 2.9 ångström (A) resolution. Compared to rhodopsin, opsin shows prominent structural changes in the conserved E(D)RY and NPxxY(x)(5,6)F regions and in TM5-TM7. At the cytoplasmic side, TM6 is tilted outwards by 6-7 A, whereas the helix structure of TM5 is more elongated and close to TM6. These structural changes, some of which were attributed to an active GPCR state, reorganize the empty retinal-binding pocket to disclose two openings that may serve the entry and exit of retinal. The opsin structure sheds new light on ligand binding to GPCRs and on GPCR activation.

---

Organizational Affiliation: 

Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Rhodopsin	A, B	348	Bos taurus	Mutation(s): 0  Gene Names: RHO
Membrane protein mpstruct	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs)	Protein:  Rhodopsin
Find proteins for P02699 (Bos taurus) Go to Gene View: RHO Go to UniProtKB:  P02699

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
BGL	A, B	B-2-OCTYLGLUCOSIDE C14 H28 O6 BVHPDIWLWHHJPD-RKQHYHRCSA-N
BMA	A, B	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PLM	A, B	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.266 
• R-Value Work: 0.229 
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 242.917	α = 90.00
b = 242.918	β = 90.00
c = 110.420	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PHASER	phasing
HKL-2000	data scaling
CNS	refinement
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-20 
• Released Date: 2008-06-24 
• Deposition Author(s): Park, J.H., Scheerer, P., Hofmann, K.P., Choe, H.-W., Ernst, O.P.

Revision History 

• Version 1.0: 2008-06-24
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Non-polymer description, Version format compliance