5C1M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • DOI: 10.1038/nature14886

  • 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 morphi ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mu-type opioid receptor
A
296Mus musculusMutation(s): 0 
Gene Names: Oprm1 (Mor, Oprm)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
μ-opioid receptor bound to a morphinan antagonist
Find proteins for P42866 (Mus musculus)
Go to UniProtKB:  P42866
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nanobody 39
B
125N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
P6G
Query on P6G

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Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
4VO
Query on 4VO

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Download CCD File 
A
(2S,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
BU72
C28 H32 N2 O2
RGJHUVJQGAAZLK-CLYKQLRXSA-N
 Ligand Interaction
CLR
Query on CLR

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Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.430α = 90.00
b = 144.000β = 90.00
c = 209.900γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug AbuseUnited StatesR37DA036246
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM083118

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references
  • Version 1.2: 2015-08-26
    Type: Data collection
  • Version 1.3: 2015-09-02
    Type: Database references
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations