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 6DDF | pdb_00006ddf

Mu Opioid Receptor-Gi Protein Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6DDF

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

Literature

Structure of the mu-opioid receptor-Giprotein complex.

Koehl, A., Hu, H., Maeda, S., Zhang, Y., Qu, Q., Paggi, J.M., Latorraca, N.R., Hilger, D., Dawson, R., Matile, H., Schertler, G.F.X., Granier, S., Weis, W.I., Dror, R.O., Manglik, A., Skiniotis, G., Kobilka, B.K.

(2018) Nature 558: 547-552

  • DOI: https://doi.org/10.1038/s41586-018-0219-7
  • Primary Citation Related Structures: 
    6DDE, 6DDF

  • PubMed Abstract: 

    The μ-opioid receptor (μOR) is a G-protein-coupled receptor (GPCR) and the target of most clinically and recreationally used opioids. The induced positive effects of analgesia and euphoria are mediated by μOR signalling through the adenylyl cyclase-inhibiting heterotrimeric G protein G i . Here we present the 3.5 Å resolution cryo-electron microscopy structure of the μOR bound to the agonist peptide DAMGO and nucleotide-free G i . DAMGO occupies the morphinan ligand pocket, with its N terminus interacting with conserved receptor residues and its C terminus engaging regions important for opioid-ligand selectivity. Comparison of the μOR-G i complex to previously determined structures of other GPCRs bound to the stimulatory G protein G s reveals differences in the position of transmembrane receptor helix 6 and in the interactions between the G protein α-subunit and the receptor core. Together, these results shed light on the structural features that contribute to the G i protein-coupling specificity of the µOR.


  • Organizational Affiliation: 
    • Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 126.46 kDa 
  • Atom Count: 6,808 
  • Modeled Residue Count: 892 
  • Deposited Residue Count: 1,130 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Entity Groups
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UniProt GroupP63096
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1344Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Mu-type opioid receptorD [auth R]356Mus 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
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UniProt GroupP42866
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DAMGOE [auth D]5Homo sapiensMutation(s): 0 
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
DAL
Query on DAL
E [auth D]D-PEPTIDE LINKINGC3 H7 N O2

--

MEA
Query on MEA
E [auth D]L-PEPTIDE LINKINGC10 H13 N O2PHE

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM007276
Swiss National Science FoundationSwitzerland310030_153145
Swiss National Science FoundationSwitzerland310030B_17335

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-10-30
    Changes: Data collection, Structure summary