4N6H

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome b562, Delta-type opioid receptor chimeric proteinA414Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 4 
Gene Names: OPRDOPRD1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41143 (Homo sapiens)
Explore P41143 
Go to UniProtKB:  P41143
PHAROS:  P41143
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EJ4
Query on EJ4

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
OLC
Query on OLC

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
OLA
Query on OLA

Download Ideal Coordinates CCD File 
B [auth A] , C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , J [auth A] , K [auth A] , 
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
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
N [auth A], O [auth A], V [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
TLA
Query on TLA

Download Ideal Coordinates CCD File 
S [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
U [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EJ4Kd :  0.5199999809265137   nM  PDBBind
EJ4Ki:  0.30000001192092896   nM  BindingDB
EJ4Ki:  0.2199999988079071   nM  BindingDB
EJ4Ki:  0.029999999329447746   nM  BindingDB
EJ4Ki:  0.8999999761581421   nM  BindingDB
EJ4Ki:  2.630000114440918   nM  BindingDB
EJ4Ki:  0.3100000023841858   nM  BindingDB
EJ4Ki:  0.20000000298023224   nM  BindingDB
EJ4Ki:  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 = 86.23α = 90
b = 72.851β = 107.48
c = 84.408γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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