Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52088.38 
• Atom Count: 3481 
• Residue Count: 414 
• Unique protein chains: 1

4N6H

1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)

• DOI: 10.2210/pdb4N6H/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 4 


• Deposited: 2013-10-12 Released: 2013-12-25 
• Deposition Author(s): Fenalti, G., Giguere, P.M., Katritch, V., Huang, X.-P., Thompson, A.A., Han, G.W., Cherezov, V., Roth, B.L., Stevens, R.C., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.190 
• R-Value Work: 0.172 

Literature

Molecular control of delta-opioid receptor signalling.

Fenalti, G., Giguere, P.M., Katritch, V., Huang, X.P., Thompson, A.A., Cherezov, V., Roth, B.L., Stevens, R.C.

(2014) Nature 506: 191-196

• PubMed: 24413399 
• DOI: 10.1038/nature12944


• PubMed Abstract: 
  

Opioids represent widely prescribed and abused medications, although their signal transduction mechanisms are not well understood. Here we present the 1.8 Å high-resolution crystal structure of the human δ-opioid receptor (δ-OR), revealing the presence and fundamental role of a sodium ion in mediating allosteric control of receptor functional selectivity and constitutive activity. The distinctive δ-OR sodium ion site architecture is centrally located in a polar interaction network in the seven-transmembrane bundle core, with the sodium ion stabilizing a reduced agonist affinity state, and thereby modulating signal transduction. Site-directed mutagenesis and functional studies reveal that changing the allosteric sodium site residue Asn 131 to an alanine or a valine augments constitutive β-arrestin-mediated signalling. Asp95Ala, Asn310Ala and Asn314Ala mutations transform classical δ-opioid antagonists such as naltrindole into potent β-arrestin-biased agonists. The data establish the molecular basis for allosteric sodium ion control in opioid signalling, revealing that sodium-coordinating residues act as 'efficacy switches' at a prototypic G-protein-coupled receptor.

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Organizational Affiliation: 

1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA [2].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Soluble cytochrome b562, Delta-type opioid receptor chimeric protein	A	414	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 4  Gene Names: cybC, OPRD1 (OPRD)
Membrane protein mpstruct	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs)	Protein:  δ-opioid receptor in complex with naltrindol
Find proteins for P0ABE7 (Escherichia coli) Go to UniProtKB:  P0ABE7
Find proteins for P41143 (Homo sapiens) Go to Gene View: OPRD1 Go to UniProtKB:  P41143

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OLC	A	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 1-Oleoyl-R-glycerol C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
OLA	A	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
TLA	A	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
PGE	A	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EJ4	A	(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol Naltrindole C26 H26 N2 O3 WIYUZYBFCWCCQJ-IFKAHUTRSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EJ4	Ki: 0 - 2.6 nM (98) BINDINGDB
EJ4	Kd: 0.52 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.190 
• R-Value Work: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 86.230	α = 90.00
b = 72.851	β = 107.48
c = 84.408	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing
Blu-Ice	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-12 
• Released Date: 2013-12-25 
• Deposition Author(s): Fenalti, G., Giguere, P.M., Katritch, V., Huang, X.-P., Thompson, A.A., Han, G.W., Cherezov, V., Roth, B.L., Stevens, R.C., GPCR Network (GPCR)

Revision History 

• Version 1.0: 2013-12-25
  Type: Initial release
• Version 1.1: 2014-01-08
  Type: Database references
• Version 1.2: 2014-03-05
  Type: Database references, Structure summary
• Version 1.3: 2017-08-02
  Type: Refinement description, Source and taxonomy
• Version 1.4: 2017-11-15
  Type: Refinement description