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- PDB-6ol9: Structure of the M5 muscarinic acetylcholine receptor (M5-T4L) bo... -

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Basic information

Entry
Database: PDB / ID: 6ol9
TitleStructure of the M5 muscarinic acetylcholine receptor (M5-T4L) bound to tiotropium
ComponentsMuscarinic acetylcholine receptor M5, T4 Lysozyme fusion
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GPCR inhibitor complex / MEMBRANE PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of phosphatidylinositol dephosphorylation / gastric acid secretion / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / dopamine transport / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / phosphatidylinositol phospholipase C activity / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / transmission of nerve impulse ...regulation of phosphatidylinositol dephosphorylation / gastric acid secretion / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / dopamine transport / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / phosphatidylinositol phospholipase C activity / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / transmission of nerve impulse / plasma membrane => GO:0005886 / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / viral release from host cell by cytolysis / peptidoglycan catabolic process / G protein-coupled acetylcholine receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / chemical synaptic transmission / postsynaptic membrane / G alpha (q) signalling events / host cell cytoplasm / defense response to bacterium / G protein-coupled receptor signaling pathway / dendrite / synapse / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M5 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...Muscarinic acetylcholine receptor M5 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-0HK / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Endolysin / Muscarinic acetylcholine receptor M5
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.541 Å
AuthorsVuckovic, Z. / Christopoulos, A. / Thal, D.M.
Funding support United Kingdom, Australia, 2items
OrganizationGrant numberCountry
Wellcome Trust201529/Z/16/Z United Kingdom
National Health and Medical Research Council (NHMRC, Australia)APP1138448 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Crystal structure of the M5muscarinic acetylcholine receptor.
Authors: Vuckovic, Z. / Gentry, P.R. / Berizzi, A.E. / Hirata, K. / Varghese, S. / Thompson, G. / van der Westhuizen, E.T. / Burger, W.A.C. / Rahmani, R. / Valant, C. / Langmead, C.J. / Lindsley, C.W. ...Authors: Vuckovic, Z. / Gentry, P.R. / Berizzi, A.E. / Hirata, K. / Varghese, S. / Thompson, G. / van der Westhuizen, E.T. / Burger, W.A.C. / Rahmani, R. / Valant, C. / Langmead, C.J. / Lindsley, C.W. / Baell, J.B. / Tobin, A.B. / Sexton, P.M. / Christopoulos, A. / Thal, D.M.
History
DepositionApr 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M5, T4 Lysozyme fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7346
Polymers55,0941
Non-polymers1,6405
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.060, 63.310, 91.620
Angle α, β, γ (deg.)90.000, 102.110, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Muscarinic acetylcholine receptor M5, T4 Lysozyme fusion / Lysis protein / Lysozyme / Muramidase


Mass: 55093.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: CHRM5, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08912, UniProt: D9IEF7, lysozyme

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Non-polymers , 5 types, 12 molecules

#2: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-0HK / (1R,2R,4S,5S,7S)-7-{[hydroxy(dithiophen-2-yl)acetyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane / Tiotropium / Tiotropium bromide


Mass: 392.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22NO4S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#4: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Reconstituted in 10:1 monoolein:cholesterol mix, 100 mM D-L Malic acid pH 6.0, 220-280 mM ammonium tartrate dibasic, 37-41% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 22, 2018
RadiationMonochromator: f / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→48.07 Å / Num. obs: 17944 / % possible obs: 100 % / Redundancy: 56.5 % / Biso Wilson estimate: 66.71 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.302 / Rpim(I) all: 0.039 / Net I/σ(I): 13.6
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 41.9 % / Num. unique obs: 2167 / Rpim(I) all: 0.533 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U15

4u15


Resolution: 2.541→47.903 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 882 4.92 %
Rwork0.2362 17046 -
obs0.2372 17928 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.15 Å2 / Biso mean: 93.8622 Å2 / Biso min: 35.96 Å2
Refinement stepCycle: final / Resolution: 2.541→47.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 105 7 3279
Biso mean--86.77 62.99 -
Num. residues----416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5414-2.70060.29851440.2756268195
2.7006-2.90910.28651600.25272845100
2.9091-3.20180.26891380.24262864100
3.2018-3.6650.2371470.23822850100
3.665-4.61690.25831500.21812866100
4.6169-47.90.2511430.24012940100
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)
13.0944-0.0025-0.89992.69780.46694.16960.0090.0157-0.0460.205-0.1221-0.08740.40120.13040.14390.4129-0.0139-0.06240.3718-0.02950.36230.82718.904-46.705
24.1451-0.1867-2.25094.28373.03983.24590.16091.31370.4685-1.3665-0.2134-0.0666-1.85620.24120.00030.83390.01610.07620.83880.07660.629843.73131.234-67.005
36.98333.73893.5898.6242-3.35786.05090.46560.694-0.1032-2.05380.5891-1.22840.84940.6676-0.87130.83370.10790.19581.48080.02130.960556.18821.5-73.76
42.55441.07294.56643.7180.40079.3077-1.0556-0.1251.4293-0.9315-0.53510.05790.27450.23611.11570.578-0.20850.13081.54530.00520.9757.42832.898-82.042
53.44811.86511.32363.6668-0.16332.32030.04420.4441-0.3177-2.29990.4024-1.0673-0.78940.5689-0.36761.97280.26860.53471.32780.01290.923549.36326.556-97.263
66.751-1.1209-1.34944.91283.08432.09260.3307-0.0383-1.2015-2.1358-0.01320.50340.2092-1.3891-0.16451.8108-0.07550.13011.02850.07140.871540.43120.77-91.583
72.10760.4068-2.15573.74820.81834.88720.28620.8042-0.0125-0.36370.07520.053-0.00510.4622-0.42780.42680.0082-0.05260.6918-0.04310.445735.53330.803-57.017
84.3546-0.1483-0.51113.67860.35146.59730.1250.810.1868-0.1018-0.21490.24050.0551-0.2660.00050.36580.09360.02820.5066-0.03810.443624.94329.117-50.09
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 26:202 )A26 - 202
2X-RAY DIFFRACTION2( CHAIN A AND RESID 203-224 or 1001:1009 )A203 - 224
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1010:1029 )A1010 - 1029
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1030:1078 )A1030 - 1078
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1079:1124 )A1079 - 1124
6X-RAY DIFFRACTION6( CHAIN A AND RESID 1125:1157 )A1125 - 1157
7X-RAY DIFFRACTION7( CHAIN A AND RESID 466:1158 )A466 - 1158
8X-RAY DIFFRACTION8( CHAIN A AND RESID 467:513 )A467 - 513
9X-RAY DIFFRACTION2( CHAIN A AND RESID 203-224 or 1001:1009 )A1001 - 1009

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