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- PDB-10tm: Cryo-EM structure of MOR bound with DAMGO -

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Basic information

Entry
Database: PDB / ID: 10tm
TitleCryo-EM structure of MOR bound with DAMGO
Components
  • Mu-type opioid receptor
  • TYR-DAL-GLY-MEA-ETA
KeywordsMEMBRANE PROTEIN / GPCR / pain relief / G protein pathway / active state
Function / homology
Function and homology information


Opioid Signalling / beta-endorphin receptor activity / morphine receptor activity / negative regulation of Wnt protein secretion / regulation of cellular response to stress / G protein-coupled opioid receptor signaling pathway / negative regulation of nitric oxide biosynthetic process / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / behavioral response to ethanol / regulation of NMDA receptor activity ...Opioid Signalling / beta-endorphin receptor activity / morphine receptor activity / negative regulation of Wnt protein secretion / regulation of cellular response to stress / G protein-coupled opioid receptor signaling pathway / negative regulation of nitric oxide biosynthetic process / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / behavioral response to ethanol / regulation of NMDA receptor activity / neuropeptide binding / positive regulation of neurogenesis / sensory perception / negative regulation of cytosolic calcium ion concentration / G-protein alpha-subunit binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / voltage-gated calcium channel activity / MECP2 regulates neuronal receptors and channels / sensory perception of pain / Peptide ligand-binding receptors / neuropeptide signaling pathway / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G-protein activation / G-protein beta-subunit binding / Interleukin-4 and Interleukin-13 signaling / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / perikaryon / positive regulation of ERK1 and ERK2 cascade / endosome / neuron projection / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / axon / synapse / dendrite / endoplasmic reticulum / Golgi apparatus / plasma membrane
Similarity search - Function
Mu opioid receptor / Opioid receptor / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
DAMGO / CHOLESTEROL / Mu-type opioid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhang, H. / Wacker, D. / Zilberg, G. / Warren, A.L. / Parpounas, A.K. / Abraham, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA) United States
CitationJournal: To Be Published
Title: cryo-EM structure of MOR-Gi1 complex protein bound with DAMGO
Authors: Zhang, H. / Wacker, D. / Zilberg, G. / Warren, A.L. / Parpounas, A.K. / Abraham, A.
History
DepositionFeb 8, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Mu-type opioid receptor
S: TYR-DAL-GLY-MEA-ETA
F: Mu-type opioid receptor
H: TYR-DAL-GLY-MEA-ETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7298
Polymers88,1834
Non-polymers1,5474
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Mu-type opioid receptor / M-OR-1 / MOR-1 / Mu opiate receptor / Mu opioid receptor / MOP / hMOP


Mass: 43577.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPRM1, MOR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35372
#2: Protein/peptide TYR-DAL-GLY-MEA-ETA


Type: Peptide-like / Class: Synthetic opioid / Mass: 513.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: DAMGO
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mu-opioid receptor complexed with orthosteric ligand DAMGO
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4110 nm / Nominal defocus min: 460 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 25.97 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX(1.19.2_4158: ???)model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 791402 / Symmetry type: POINT
RefinementResolution: 3→3 Å / SU ML: 0.21 / σ(F): 1.15 / Phase error: 55.85 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3342 1966 0.19 %
Rwork0.33 --
obs0.33 1019863 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00614710
ELECTRON MICROSCOPYf_angle_d0.76620016
ELECTRON MICROSCOPYf_dihedral_angle_d13.2665342
ELECTRON MICROSCOPYf_chiral_restr0.0472352
ELECTRON MICROSCOPYf_plane_restr0.0052472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.44651320.409872232ELECTRON MICROSCOPY100
3.59-3.680.41331440.362673053ELECTRON MICROSCOPY100
3.68-3.790.28981560.341572764ELECTRON MICROSCOPY100
3.79-3.920.37371260.323972964ELECTRON MICROSCOPY100
3.92-4.060.30091320.313972943ELECTRON MICROSCOPY100
4.06-4.220.31311140.308172754ELECTRON MICROSCOPY100
4.22-4.410.2561680.290872361ELECTRON MICROSCOPY100
4.41-4.640.26771680.266872974ELECTRON MICROSCOPY100
4.64-4.930.30351180.269172544ELECTRON MICROSCOPY100
4.93-5.310.30791560.320372829ELECTRON MICROSCOPY100
5.31-5.850.37241320.372772742ELECTRON MICROSCOPY100
5.85-6.690.47161200.407972797ELECTRON MICROSCOPY100
6.7-8.430.38721560.380972692ELECTRON MICROSCOPY100
8.44-275.460.34741440.343872248ELECTRON MICROSCOPY99

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