Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 55.76 kDa 
• Atom Count: 3690 
• Modelled Residue Count: 442 
• Deposited Residue Count: 464 
• Unique protein chains: 1

4DKL

Crystal structure of the mu-opioid receptor bound to a morphinan antagonist

• DOI: 10.2210/pdb4DKL/pdb

• Classification: SIGNALING PROTEIN/ANTAGONIST
• Organism(s): Mus musculus, Escherichia virus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-02-03 Released: 2012-03-21 
• Deposition Author(s): Manglik, A., Kruse, A.C., Kobilka, T.S., Thian, F.S., Mathiesen, J.M., Sunahara, R.K., Pardo, L., Weis, W.I., Kobilka, B.K., Granier, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.275 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

Literature

Crystal structure of the {mu}-opioid receptor bound to a morphinan antagonist.

Manglik, A., Kruse, A.C., Kobilka, T.S., Thian, F.S., Mathiesen, J.M., Sunahara, R.K., Pardo, L., Weis, W.I., Kobilka, B.K., Granier, S.

(2012) Nature 485: 321-326

• PubMed: 22437502 
• DOI: 10.1038/nature10954
• Primary Citation of Related Structures:  
  4DKL


• PubMed Abstract: 
  

Opium is one of the world's oldest drugs, and its derivatives morphine and codeine are among the most used clinical drugs to relieve severe pain. These prototypical opioids produce analgesia as well as many undesirable side effects (sedation, apnoea and dependence) by binding to and activating the G-protein-coupled µ-opioid receptor (µ-OR) in the central nervous system. Here we describe the 2.8 Å crystal structure of the mouse µ-OR in complex with an irreversible morphinan antagonist. Compared to the buried binding pocket observed in most G-protein-coupled receptors published so far, the morphinan ligand binds deeply within a large solvent-exposed pocket. Of particular interest, the µ-OR crystallizes as a two-fold symmetrical dimer through a four-helix bundle motif formed by transmembrane segments 5 and 6. These high-resolution insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction.

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Organizational Affiliation: 

Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mu-type opioid receptor, lysozyme chimera	A	464	Mus musculus, Escherichia virus T4	Mutation(s): 3  Gene Names: Mor, Oprm, Oprm1, E EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors: Class A	Protein:  μ-opioid receptor bound to a morphinan antagonist
Find proteins for P42866 (Mus musculus) Explore P42866  Go to UniProtKB:  P42866
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BF0	B [auth A]	methyl 4-{[(5beta,6alpha)-17-(cyclopropylmethyl)-3,14-dihydroxy-4,5-epoxymorphinan-6-yl]amino}-4-oxobutanoate C25 H32 N2 O6 PGIBGSVRAVGQMY-OIUZVZFJSA-N
CLR	O [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
MPG	P [auth A], Q [auth A]	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C21 H40 O4 JPJYKWFFJCWMPK-GDCKJWNLSA-N
1PE	R [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	S [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.275 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.882	α = 90
b = 174.73	β = 107.84
c = 68.353	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-03 
• Released Date: 2012-03-21 
Deposition Author(s): Manglik, A., Kruse, A.C., Kobilka, T.S., Thian, F.S., Mathiesen, J.M., Sunahara, R.K., Pardo, L., Weis, W.I., Kobilka, B.K., Granier, S.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2012-05-16
  Changes: Database references
• Version 1.2: 2016-06-08
  Changes: Atomic model
• Version 1.3: 2017-07-26
  Changes: Refinement description, Source and taxonomy