2X72

CRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,D2C,D282C RHODOPSIN MUTANT WITH BOUND GALPHACT PEPTIDE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report



Literature

The Structural Basis of Agonist Induced Activation in Constitutively Active Rhodopsin

Standfuss, J.Edwards, P.C.Dantona, A.Fransen, M.Xie, G.Oprian, D.D.Schertler, G.F.X.

(2011) Nature 471: 656

  • DOI: 10.1038/nature09795
  • Primary Citation of Related Structures:  
    2X72

  • PubMed Abstract: 
  • G-protein-coupled receptors (GPCRs) comprise the largest family of membrane proteins in the human genome and mediate cellular responses to an extensive array of hormones, neurotransmitters and sensory stimuli. Although some crystal structures have be ...

    G-protein-coupled receptors (GPCRs) comprise the largest family of membrane proteins in the human genome and mediate cellular responses to an extensive array of hormones, neurotransmitters and sensory stimuli. Although some crystal structures have been determined for GPCRs, most are for modified forms, showing little basal activity, and are bound to inverse agonists or antagonists. Consequently, these structures correspond to receptors in their inactive states. The visual pigment rhodopsin is the only GPCR for which structures exist that are thought to be in the active state. However, these structures are for the apoprotein, or opsin, form that does not contain the agonist all-trans retinal. Here we present a crystal structure at a resolution of 3 Å for the constitutively active rhodopsin mutant Glu 113 Gln in complex with a peptide derived from the carboxy terminus of the α-subunit of the G protein transducin. The protein is in an active conformation that retains retinal in the binding pocket after photoactivation. Comparison with the structure of ground-state rhodopsin suggests how translocation of the retinal β-ionone ring leads to a rotation of transmembrane helix 6, which is the critical conformational change on activation. A key feature of this conformational change is a reorganization of water-mediated hydrogen-bond networks between the retinal-binding pocket and three of the most conserved GPCR sequence motifs. We thus show how an agonist ligand can activate its GPCR.


    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

    Organizational Affiliation

    Paul Scherrer Institut, 5232 Villigen PSI, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RHODOPSINA349Bos taurusMutation(s): 3 
Gene Names: RHO
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
Rhodopsin in agonist-induced active state
Find proteins for P02699 (Bos taurus)
Explore P02699 
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-1B11Bos 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 agonist-induced active 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
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
5 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEF
Query on PEF

Download Ideal Coordinates CCD File 
A
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
LPP
Query on LPP

Download Ideal Coordinates CCD File 
A
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
C35 H69 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-N
 Ligand Interaction
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

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A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
PLM
Query on PLM

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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: 3.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 243.986α = 90
b = 243.986β = 90
c = 109.156γ = 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: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary