Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.09 kDa 
• Atom Count: 3582 
• Modelled Residue Count: 408 
• Deposited 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): Yes 
• Membrane Protein: Yes  OPMPDBTM


• 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: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

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
• Primary Citation of Related Structures:  
  4N6H


• 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: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562, Delta-type opioid receptor chimeric protein	A	414	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 4  Gene Names: OPRD, OPRD1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41143 (Homo sapiens) Explore P41143  Go to UniProtKB:  P41143
PHAROS:  P41143 GTEx:  ENSG00000116329
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EJ4	T [auth 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 C26 H26 N2 O3 WIYUZYBFCWCCQJ-IFKAHUTRSA-N
OLC	H [auth A], I [auth A], M [auth A], W [auth A], X [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	B [auth A],  C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  J [auth A],  K [auth A],  L [auth A],  P [auth A],  Q [auth A],  R [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PGE	N [auth A], O [auth A], V [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TLA	S [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
NA	U [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EJ4	Kd :  0.5199999809265137   nM  PDBBind
EJ4	Ki:  0.30000001192092896   nM  BindingDB
EJ4	Ki:  0.2199999988079071   nM  BindingDB
EJ4	Ki:  0.029999999329447746   nM  BindingDB
EJ4	Ki:  0.8999999761581421   nM  BindingDB
EJ4	Ki:  2.630000114440918   nM  BindingDB
EJ4	Ki:  0.3100000023841858   nM  BindingDB
EJ4	Ki:  0.20000000298023224   nM  BindingDB
EJ4	Ki:  0.46000000834465027   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.23	α = 90
b = 72.851	β = 107.48
c = 84.408	γ = 90

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2014-03-05
  Changes: Database references, Structure summary
• Version 1.3: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2017-11-15
  Changes: Refinement description