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 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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
  • Also Cited By: 4A4M

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RHODOPSIN
A
349Bos taurusGene Names: RHO
Membrane protein
mpstruct
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-1
B
11Bos taurusGene Names: GNAT1
Membrane protein
mpstruct
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 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PEF
Query on PEF

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A
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
RET
Query on RET

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

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
LPP
Query on LPP

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A
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE; L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT; 3-SN-PHOSPHATIDIC ACID; 1,2-DIPALMITOYLDISODIUM SALT
C35 H69 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PLM
Query on PLM

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A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
BOG
Query on BOG

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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 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 243.986α = 90.00
b = 243.986β = 90.00
c = 109.156γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance