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


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 

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This is version 2.0 of the entry. See complete history


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

  • 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* ...

    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.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RhodopsinA348Bos taurusMutation(s): 0 
Gene Names: RHO
Membrane Entity: Yes 
UniProt
Find proteins for P02699 (Bos taurus)
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Go to UniProtKB:  P02699
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
11meric peptide form Guanine nucleotide-binding protein G(t) subunit alpha-1B11N/AMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P04695 (Bos taurus)
Explore P04695 
Go to UniProtKB:  P04695
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseC4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
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 = 238.02α = 90
b = 238.02β = 90
c = 109.132γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
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: 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