Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 42.86 kDa 
• Atom Count: 2866 
• Modelled Residue Count: 337 
• Deposited Residue Count: 359 
• Unique protein chains: 2

3DQB

Crystal structure of the active G-protein-coupled receptor opsin in complex with a C-terminal peptide derived from the Galpha subunit of transducin

• PDB DOI: 10.2210/pdb3DQB/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2008-07-09 Released: 2008-09-23 
• Deposition Author(s): Scheerer, P., Park, J.H., Hildebrand, P.W., Kim, Y.J., Krauss, N., Choe, H.-W., Hofmann, K.P., Ernst, O.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Crystal structure of opsin in its G-protein-interacting conformation

Scheerer, P., Park, J.H., Hildebrand, P.W., Kim, Y.J., Krauss, N., Choe, H.-W., Hofmann, K.P., Ernst, O.P.

(2008) Nature 455: 497-502

• PubMed: 18818650 
• DOI: 10.1038/nature07330
• Primary Citation of Related Structures:  
  3DQB


• PubMed Abstract: 
  

Opsin, the ligand-free form of the G-protein-coupled receptor rhodopsin, at low pH adopts a conformationally distinct, active G-protein-binding state known as Ops*. A synthetic peptide derived from the main binding site of the heterotrimeric G protein-the carboxy terminus of the alpha-subunit (GalphaCT)-stabilizes Ops*. Here we present the 3.2 A crystal structure of the bovine Ops*-GalphaCT peptide complex. GalphaCT binds to a site in opsin that is opened by an outward tilt of transmembrane helix (TM) 6, a pairing of TM5 and TM6, and a restructured TM7-helix 8 kink. Contacts along the inner surface of TM5 and TM6 induce an alpha-helical conformation in GalphaCT with a C-terminal reverse turn. Main-chain carbonyl groups in the reverse turn constitute the centre of a hydrogen-bonded network, which links the two receptor regions containing the conserved E(D)RY and NPxxY(x)(5,6)F motifs. On the basis of the Ops*-GalphaCT structure and known conformational changes in Galpha, we discuss signal transfer from the receptor to the G protein nucleotide-binding site.

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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	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
11meric peptide form Guanine nucleotide-binding protein G(t) subunit alpha-1	B	11	N/A	Mutation(s): 1  Membrane Entity: Yes
UniProt
Find proteins for P04695 (Bos taurus) Explore P04695  Go to UniProtKB:  P04695

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-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	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	E [auth A], F [auth A], G [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM	H [auth A], I [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 238.02	α = 90
b = 238.02	β = 90
c = 109.132	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-09 
• Released Date: 2008-09-23 
Deposition Author(s): Scheerer, P., Park, J.H., Hildebrand, P.W., Kim, Y.J., Krauss, N., Choe, H.-W., Hofmann, K.P., Ernst, O.P.

Revision History  

• Version 1.0: 2008-09-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2014-02-05
  Changes: Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Structure summary