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- PDB-8e0g: Re-refined model of active mu-opioid receptor (PDB 5c1m) as an ad... -

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Basic information

Entry
Database: PDB / ID: 8e0g
TitleRe-refined model of active mu-opioid receptor (PDB 5c1m) as an adduct with BU72
Components
  • Mu-type opioid receptor
  • Nanobody 39
KeywordsSIGNALING PROTEIN/AGONIST / Agonist / Active State / Revised Structure / SIGNALING PROTEIN-AGONIST complex
Function / homology
Function and homology information


Opioid Signalling / spine apparatus / beta-endorphin receptor activity / morphine receptor activity / negative regulation of Wnt protein secretion / Peptide ligand-binding receptors / adenylate cyclase-inhibiting opioid receptor signaling pathway / positive regulation of appetite / G-protein activation / G protein-coupled opioid receptor activity ...Opioid Signalling / spine apparatus / beta-endorphin receptor activity / morphine receptor activity / negative regulation of Wnt protein secretion / Peptide ligand-binding receptors / adenylate cyclase-inhibiting opioid receptor signaling pathway / positive regulation of appetite / G-protein activation / G protein-coupled opioid receptor activity / negative regulation of luteinizing hormone secretion / G protein-coupled opioid receptor signaling pathway / sperm ejaculation / G alpha (i) signalling events / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / negative regulation of nitric oxide biosynthetic process / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / neuropeptide binding / negative regulation of cAMP-mediated signaling / regulation of NMDA receptor activity / positive regulation of neurogenesis / eating behavior / negative regulation of cytosolic calcium ion concentration / transmission of nerve impulse / social behavior / G-protein alpha-subunit binding / GABA-ergic synapse / voltage-gated calcium channel activity / neuropeptide signaling pathway / positive regulation of gluconeogenesis / sensory perception of pain / dendrite membrane / presynaptic modulation of chemical synaptic transmission / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / excitatory postsynaptic potential / dendrite cytoplasm / locomotory behavior / G protein-coupled receptor activity / adenylate cyclase-activating dopamine receptor signaling pathway / G-protein beta-subunit binding / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / postsynaptic membrane / perikaryon / response to ethanol / positive regulation of ERK1 and ERK2 cascade / endosome / neuron projection / G protein-coupled receptor signaling pathway / protein domain specific binding / axon / focal adhesion / dendrite / membrane / plasma membrane
Similarity search - Function
Mu opioid receptor / Opioid receptor / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Chem-VF1 / Mu-type opioid receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMunro, T.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2015
Title: Structural insights into mu-opioid receptor activation.
Authors: 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. / ...Authors: 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.
History
DepositionAug 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Advisory / Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_database_remark / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _pdbx_database_remark.text / _struct_conn.pdbx_leaving_atom_flag
Remark 0THIS ENTRY 8E0G REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5C1M, DETERMINED BY W.J. ...THIS ENTRY 8E0G REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5C1M, DETERMINED BY W.J.HUANG,A.MANGLIK,A.J.VENKATAKRISHNAN,T.LAEREMANS,E.N.FEINBERG,A.L.SANBORN,H.E.KATO,K.E.LIVINGSTON,T.S.THORSEN,R.KLING,S.GRANIER,P.GMEINER,S.M.HUSBANDS,J.R.TRAYNOR,W.I.WEIS,J.STEYAERT,R.O.DROR,B.K.KOBILKA

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mu-type opioid receptor
B: Nanobody 39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4039
Polymers47,3032
Non-polymers2,1007
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: As in original entry 5C1M v2.0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-21 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.430, 144.000, 209.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Protein / Antibody , 2 types, 2 molecules AB

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


Mass: 33745.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Oprm1, Mor, Oprm / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P42866
#2: Antibody Nanobody 39


Mass: 13558.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 75 molecules

#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-VF1 / (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 / BU72


Mass: 428.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C28H32N2O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1 / Details: AUTHOR USED THE SF DATA FROM ENTRY 5C1M.

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.78 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5C1M
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: Reconstituted in 10:1 monoolein:cholesterol mix, precipitant: 15-25% PEG300, 100 mM HEPES, pH 7.0-7.5, 1% 1,2,3-heptanetriol, 0.5-1.0% polypropylene glycol P400, 100-300 mM ammonium phosphate dibasic
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→43.5 Å / Num. obs: 40051 / % possible obs: 99.5 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 7.51
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.4451 / Num. unique obs: 4399 / % possible all: 95

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Processing

SoftwareName: PDB-REDO / Version: 7.32 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5C1M

5c1m


Resolution: 2.1→43.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.842 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22548 1999 5 %RANDOM
Rwork0.1915 ---
obs0.19319 37971 99.8 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.315 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0 Å2-0 Å2
2--3.63 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 99 68 3475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0183533
X-RAY DIFFRACTIONr_bond_other_d0.0010.023351
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.8674819
X-RAY DIFFRACTIONr_angle_other_deg1.3592.8757731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77922.045132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25815553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.431522
X-RAY DIFFRACTIONr_chiral_restr0.1460.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
X-RAY DIFFRACTIONr_mcbond_it2.9142.0421673
X-RAY DIFFRACTIONr_mcbond_other2.9112.041672
X-RAY DIFFRACTIONr_mcangle_it4.2043.0422093
X-RAY DIFFRACTIONr_mcangle_other4.2033.0452094
X-RAY DIFFRACTIONr_scbond_it4.6272.7381860
X-RAY DIFFRACTIONr_scbond_other4.6262.7421861
X-RAY DIFFRACTIONr_scangle_other6.6343.8442727
X-RAY DIFFRACTIONr_long_range_B_refined9.55326.1344040
X-RAY DIFFRACTIONr_long_range_B_other9.55325.9834026
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 146 -
Rwork0.305 2775 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.39840.2147-0.01731.893-0.28872.4634-0.08420.0050.109-0.15390.02510.0273-0.303-0.07610.05910.3337-0.0038-0.01180.0035-0.01640.4203-2.21315.626-48.184
24.1379-0.04821.2372.39880.2686.298-0.0409-0.59660.01310.1659-0.05910.0581-0.1728-0.08520.10.2758-0.01640.02050.3076-0.00980.3255-3.2059.002-11.354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 347
2X-RAY DIFFRACTION2B3 - 127

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