Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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: 82.68 kDa 
• Atom Count: 5504 
• Modelled Residue Count: 652 
• Deposited Residue Count: 696 
• Unique protein chains: 1

3CAP

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

• PDB DOI: 10.2210/pdb3CAP/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• 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: 2.90 Å
• R-Value Free: 0.266 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

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
• Primary Citation of Related Structures:  
  3CAP


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A, B	348	Bos taurus	Mutation(s): 0  Gene Names: RHO Membrane Entity: Yes
UniProt
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-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G31886NL GlyCosmos:  G31886NL GlyGen:  G31886NL

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	D, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGL	G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B]	2-O-octyl-beta-D-glucopyranose C14 H28 O6 BVHPDIWLWHHJPD-RKQHYHRCSA-N
PLM	K [auth A], N [auth B]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.266 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.917	α = 90
b = 242.918	β = 90
c = 110.42	γ = 120

Software Package:

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

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
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary