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 5C1M | pdb_00005c1m

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.229 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5C1M

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8E0G

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: https://doi.org/10.1038/nature14886
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 49.59 kDa 
  • Atom Count: 3,518 
  • Modeled Residue Count: 414 
  • Deposited Residue Count: 421 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mu-type opioid receptor296Mus musculusMutation(s): 0 
Gene Names: Oprm1, Mor, Oprm
Membrane Entity: Yes 
UniProt
Find proteins for P42866 (Mus musculus)
Explore P42866 
Go to UniProtKB:  P42866
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42866
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody 39125Lama glamaMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VF1
(Subject of Investigation/LOI)

Query on VF1



Download:Ideal Coordinates CCD File
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

Query on CLR



Download:Ideal Coordinates CCD File
E [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC

Query on OLC



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.229 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.43α = 90
b = 144β = 90
c = 209.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR37DA036246
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM083118

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description