4A4M

Crystal structure of the light-activated constitutively active N2C, M257Y,D282C rhodopsin mutant in complex with a peptide resembling the C-terminus of the Galpha-protein subunit (GaCT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report



Literature

Stabilized G Protein Binding Site in the Structure of Constitutively Active Metarhodopsin-II.

Deupi, X.Edwards, P.Singhal, A.Nickle, B.Oprian, D.Schertler, G.Standfuss, J.

(2012) Proc Natl Acad Sci U S A 109: 119

  • DOI: 10.1073/pnas.1114089108
  • Primary Citation of Related Structures:  
    4A4M

  • PubMed Abstract: 
  • G protein-coupled receptors (GPCR) are seven transmembrane helix proteins that couple binding of extracellular ligands to conformational changes and activation of intracellular G proteins, GPCR kinases, and arrestins. Constitutively active mutants ar ...

    G protein-coupled receptors (GPCR) are seven transmembrane helix proteins that couple binding of extracellular ligands to conformational changes and activation of intracellular G proteins, GPCR kinases, and arrestins. Constitutively active mutants are ubiquitously found among GPCRs and increase the inherent basal activity of the receptor, which often correlates with a pathological outcome. Here, we have used the M257Y(6.40) constitutively active mutant of the photoreceptor rhodopsin in combination with the specific binding of a C-terminal fragment from the G protein alpha subunit (GαCT) to trap a light activated state for crystallization. The structure of the M257Y/GαCT complex contains the agonist all-trans-retinal covalently bound to the native binding pocket and resembles the G protein binding metarhodopsin-II conformation obtained by the natural activation mechanism; i.e., illumination of the prebound chromophore 11-cis-retinal. The structure further suggests a molecular basis for the constitutive activity of 6.40 substitutions and the strong effect of the introduced tyrosine based on specific interactions with Y223(5.58) in helix 5, Y306(7.53) of the NPxxY motif and R135(3.50) of the E(D)RY motif, highly conserved residues of the G protein binding site.


    Related Citations: 
    • Crystal Structure of a Thermally Stable Rhodopsin Mutant.
      Standfuss, J., Xie, G., Edwards, P.C., Burghammer, M., Oprian, D.D., Schertler, G.F.X.
      (2007) J Mol Biol 372: 1179
    • The Structural Basis of Agonist-Induced Activation in Constitutively Active Rhodopsin.
      Standfuss, J., Edwards, P.C., D'Antona, A., Fransen, M., Xie, G., Oprian, D.D., Schertler, G.F.X.
      (2011) Nature 471: 656

    Organizational Affiliation

    Paul Scherrer Institut, Villigen PSI, 5232, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RHODOPSINA349Bos taurusMutation(s): 4 
Gene Names: RHO
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
Rhodopsin in constitutively active meta-II state
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
GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-3B11Bos taurusMutation(s): 1 
Gene Names: GNAT1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
Rhodopsin in constitutively active meta-II state
Find proteins for P04695 (Bos taurus)
Explore P04695 
Go to UniProtKB:  P04695
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download Ideal Coordinates CCD File 
A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
RET
Query on RET

Download Ideal Coordinates CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
PLM
Query on PLM

Download Ideal Coordinates CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.19α = 90
b = 242.19β = 90
c = 109.829γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary