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: 3.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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.USA 109: 119

  • DOI: 10.1073/pnas.1114089108

  • 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: 
    • 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
    • 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

    Organizational Affiliation: 

    Paul Scherrer Institut, Villigen PSI, 5232, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RHODOPSIN
A
349Bos taurusMutation(s): 3 
Gene Names: RHO
Membrane protein
mpstruc		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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-3
B
11Bos taurusMutation(s): 1 
Gene Names: GNAT1
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
G Protein-Coupled Receptors (GPCRs)		Protein: 
Rhodopsin
Find proteins for P04695 (Bos taurus)
Go to Gene View: GNAT1
Go to UniProtKB:  P04695
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
RET
Query on RET
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Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
NAG
Query on NAG
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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM
Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG
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Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 242.190α = 90.00
b = 242.190β = 90.00
c = 109.829γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Database references, Derived calculations, Other