Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.70 kDa 
• Atom Count: 2932 
• Residue Count: 338 
• Unique protein chains: 2

2X72

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

• DOI: 10.2210/pdb2X72/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2010-02-22 Released: 2011-03-16 
• Deposition Author(s): Standfuss, J., Edwards, P.C., Dantona, A., Fransen, M., Xie, G., Oprian, D.D., Schertler, G.F.X.

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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 

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

• PubMed: 21389983 
• 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 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.

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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

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Organizational Affiliation: 

Paul Scherrer Institut, 5232 Villigen PSI, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHODOPSIN	A	349	Bos taurus	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1	B	11	Bos taurus	Mutation(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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEF	A	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C37 H74 N O8 P SLKDGVPOSSLUAI-PGUFJCEWSA-N
LPP	A	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE C35 H69 O8 P PORPENFLTBBHSG-MGBGTMOVSA-N
BOG	A	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
RET	A	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
PLM	A	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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 = 243.986	α = 90
b = 243.986	β = 90
c = 109.156	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-22 
• Released Date: 2011-03-16 
Deposition Author(s): Standfuss, J., Edwards, P.C., Dantona, A., Fransen, M., Xie, G., Oprian, D.D., Schertler, G.F.X.

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