Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 49.59 kDa 
• Atom Count: 3518 
• Modelled Residue Count: 414 
• Deposited Residue Count: 421 
• Unique protein chains: 2

5C1M

Crystal structure of active mu-opioid receptor bound to the agonist BU72

• DOI: 10.2210/pdb5C1M/pdb

• Classification: Signaling Protein/antagonist
• Organism(s): Mus musculus, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2015-06-15 Released: 2015-08-05 
• Deposition Author(s): Huang, W.J., Manglik, A., Venkatakrishnan, A.J., Laeremans, T., Feinberg, E.N., Sanborn, A.L., Kato, H.E., Livingston, K.E., Thorsen, T.S., Kling, R., Granier, S., Gmeiner, P., Husbands, S.M., Traynor, J.R., Weis, W.I., Steyaert, J., Dror, R.O., Kobilka, B.K.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.229 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Structural insights into mu-opioid receptor activation.

Huang, W., Manglik, A., Venkatakrishnan, A.J., Laeremans, T., Feinberg, E.N., Sanborn, A.L., Kato, H.E., Livingston, K.E., Thorsen, T.S., Kling, R.C., Granier, S., Gmeiner, P., Husbands, S.M., Traynor, J.R., Weis, W.I., Steyaert, J., Dror, R.O., Kobilka, B.K.

(2015) Nature 524: 315-321

• PubMed: 26245379 
• DOI: 10.1038/nature14886
• Primary Citation of Related Structures:  
  5C1M


• PubMed Abstract: 
  

Activation of the μ-opioid receptor (μOR) is responsible for the efficacy of the most effective analgesics. To shed light on the structural basis for μOR activation, here we report a 2.1 Å X-ray crystal structure of the murine μOR bound to the morphinan agonist BU72 and a G protein mimetic camelid antibody fragment. The BU72-stabilized changes in the μOR binding pocket are subtle and differ from those observed for agonist-bound structures of the β2-adrenergic receptor (β2AR) and the M2 muscarinic receptor. Comparison with active β2AR reveals a common rearrangement in the packing of three conserved amino acids in the core of the μOR, and molecular dynamics simulations illustrate how the ligand-binding pocket is conformationally linked to this conserved triad. Additionally, an extensive polar network between the ligand-binding pocket and the cytoplasmic domains appears to play a similar role in signal propagation for all three G-protein-coupled receptors.

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Organizational Affiliation: 

Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mu-type opioid receptor	A	296	Mus musculus	Mutation(s): 0  Gene Names: Oprm1, Mor, Oprm Membrane Entity: Yes
UniProt
Find proteins for P42866 (Mus musculus) Explore P42866  Go to UniProtKB:  P42866

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 39	B	125	Lama glama	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VF1 (Subject of Investigation/LOI)	I [auth A]	(2R,3S,3aR,5aR,6R,11bR,11cS)-3a-methoxy-3,14-dimethyl-2-phenyl-2,3,3a,6,7,11c-hexahydro-1H-6,11b-(epiminoethano)-3,5a-methanonaphtho[2,1-g]indol-10-ol C28 H32 N2 O2 RGJHUVJQGAAZLK-GKTFKBBASA-N
CLR (Subject of Investigation/LOI)	E [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC (Subject of Investigation/LOI)	C [auth A], D [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
P6G	G [auth A], H [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	A	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4VO	Ki:  0.01600000075995922   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.229 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.43	α = 90
b = 144	β = 90
c = 209.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-15 
• Released Date: 2015-08-05 
Deposition Author(s): Huang, W.J., Manglik, A., Venkatakrishnan, A.J., Laeremans, T., Feinberg, E.N., Sanborn, A.L., Kato, H.E., Livingston, K.E., Thorsen, T.S., Kling, R., Granier, S., Gmeiner, P., Husbands, S.M., Traynor, J.R., Weis, W.I., Steyaert, J., Dror, R.O., Kobilka, B.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	R37DA036246
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM083118

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2015-08-19
  Changes: Database references
• Version 1.2: 2015-08-26
  Changes: Data collection
• Version 1.3: 2015-09-02
  Changes: Database references
• Version 1.4: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.5: 2019-12-11
  Changes: Author supporting evidence
• Version 2.0: 2021-02-10
  Type: Coordinate replacement
  Reason: Chirality error
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary